| Target Namespace | http://pdbml.pdb.org/schema/pdbx-validation-v4.xsd |
|---|---|
| Element and Attribute Namespaces |
|
| Documentation |
VRPT PDBML Schema translated from wwPDB Validation Information Dictionary v4.370, which is backward compatible with the PDBx/mmCIF Dictionary v5.370:
http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic
More information at: http://pdbml.pdb.org/schema/pdbx-validation-v4.xsd. |
| Application Data | VRPT PDBML Schema v4.370 |
| Prefix | Namespace |
|---|---|
| VRPTx | http://pdbml.pdb.org/schema/pdbx-validation-v4.xsd |
| xsd | http://www.w3.org/2001/XMLSchema |
| xml | http://www.w3.org/XML/1998/namespace |
| Name | datablock |
|---|---|
| Type | VRPTx:datablockType |
| Nillable | no |
| Abstract | no |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | datablockType |
|---|---|
| Abstract | no |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrnType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN category record details about the
diffraction data and their measurement.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:diffrnCategory>
<VRPTx:diffrn id="Set1">
<VRPTx:ambient_environment> Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air</VRPTx:ambient_environment>
<VRPTx:ambient_temp>293.0</VRPTx:ambient_temp>
<VRPTx:crystal_support> 0.7 mm glass capillary, sealed with dental wax</VRPTx:crystal_support>
<VRPTx:crystal_treatment> Equilibrated in rotating anode radiation enclosure for
18 hours prior to beginning of data collection</VRPTx:crystal_treatment>
</VRPTx:diffrn>
</VRPTx:diffrnCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
<VRPTx:diffrnCategory>
<VRPTx:diffrn id="d1">
<VRPTx:ambient_temp>293</VRPTx:ambient_temp>
<VRPTx:details> \q scan width (1.0 + 0.14tan\q)\%, \q scan rate 1.2\% per
min. Background counts for 5 sec on each side every scan.</VRPTx:details>
</VRPTx:diffrn>
</VRPTx:diffrnCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_attenuatorType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_ATTENUATOR category record details
about the diffraction attenuator scales employed.
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<VRPTx:diffrn_attenuatorCategory>
<VRPTx:diffrn_attenuator code="1">
<VRPTx:scale>16.976</VRPTx:scale>
</VRPTx:diffrn_attenuator>
</VRPTx:diffrn_attenuatorCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_attenuator.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_detectorType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:diffrn_detectorCategory>
<VRPTx:diffrn_detector diffrn_id="d1">
<VRPTx:detector>multiwire</VRPTx:detector>
<VRPTx:type>Siemens</VRPTx:type>
</VRPTx:diffrn_detector>
</VRPTx:diffrn_detectorCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_detector.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_measurementType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the diffraction
data were measured.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:diffrn_measurementCategory>
<VRPTx:diffrn_measurement diffrn_id="d1">
<VRPTx:details> 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm,
detector angle 22.5 degrees</VRPTx:details>
<VRPTx:device>3-circle camera</VRPTx:device>
<VRPTx:device_details>none</VRPTx:device_details>
<VRPTx:device_type>Supper model x</VRPTx:device_type>
<VRPTx:method>omega scan</VRPTx:method>
</VRPTx:diffrn_measurement>
</VRPTx:diffrn_measurementCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<VRPTx:diffrn_measurementCategory>
<VRPTx:diffrn_measurement diffrn_id="s1">
<VRPTx:device_type>Philips PW1100/20 diffractometer</VRPTx:device_type>
<VRPTx:method>\q/2\q</VRPTx:method>
</VRPTx:diffrn_measurement>
</VRPTx:diffrn_measurementCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_measurement.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_orient_matrixType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_ORIENT_MATRIX category record details
about the orientation matrix used in the measurement of the
diffraction data.
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4.
<VRPTx:diffrn_orient_matrixCategory>
<VRPTx:diffrn_orient_matrix diffrn_id="set1">
<VRPTx:UB11>-0.071479</VRPTx:UB11>
<VRPTx:UB12>0.020208</VRPTx:UB12>
<VRPTx:UB13>0.039076</VRPTx:UB13>
<VRPTx:UB21>0.035372</VRPTx:UB21>
<VRPTx:UB22>0.056209</VRPTx:UB22>
<VRPTx:UB23>0.078324</VRPTx:UB23>
<VRPTx:UB31>-0.007470</VRPTx:UB31>
<VRPTx:UB32>0.067854</VRPTx:UB32>
<VRPTx:UB33>-0.017832</VRPTx:UB33>
<VRPTx:type> reciprocal axis matrix, multiplies hkl vector to generate
diffractometer xyz vector and diffractometer angles</VRPTx:type>
</VRPTx:diffrn_orient_matrix>
</VRPTx:diffrn_orient_matrixCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_orient_matrix.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_orient_reflnType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_ORIENT_REFLN category record details
about the reflections that define the orientation matrix used in
the measurement of the diffraction intensities.
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4.
<VRPTx:diffrn_orient_reflnCategory>
<VRPTx:diffrn_orient_refln diffrn_id="myset1" index_h="2" index_k="0" index_l="2">
<VRPTx:angle_chi>-28.45</VRPTx:angle_chi>
<VRPTx:angle_kappa>-11.32</VRPTx:angle_kappa>
<VRPTx:angle_omega>5.33</VRPTx:angle_omega>
<VRPTx:angle_phi>101.78</VRPTx:angle_phi>
<VRPTx:angle_psi>0.00</VRPTx:angle_psi>
<VRPTx:angle_theta>10.66</VRPTx:angle_theta>
</VRPTx:diffrn_orient_refln>
</VRPTx:diffrn_orient_reflnCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_orient_refln.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_radiationType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_RADIATION category describe
the radiation used in measuring the diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:diffrn_radiationCategory>
<VRPTx:diffrn_radiation diffrn_id="set1">
<VRPTx:collimation>0.3 mm double pinhole</VRPTx:collimation>
<VRPTx:monochromator>graphite</VRPTx:monochromator>
<VRPTx:type>Cu K\a</VRPTx:type>
<VRPTx:wavelength_id>1</VRPTx:wavelength_id>
</VRPTx:diffrn_radiation>
</VRPTx:diffrn_radiationCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<VRPTx:diffrn_radiationCategory>
<VRPTx:diffrn_radiation diffrn_id="set1">
<VRPTx:monochromator>graphite</VRPTx:monochromator>
<VRPTx:type>Cu K\a</VRPTx:type>
<VRPTx:wavelength_id>1</VRPTx:wavelength_id>
</VRPTx:diffrn_radiation>
</VRPTx:diffrn_radiationCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_radiation.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_radiation_wavelengthType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_RADIATION_WAVELENGTH category
describe the wavelength of the radiation used to measure the
diffraction intensities. Items may be looped to identify
and assign weights to distinct components of a
polychromatic beam.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:diffrn_radiation_wavelengthCategory>
<VRPTx:diffrn_radiation_wavelength id="1">
<VRPTx:wavelength>1.54</VRPTx:wavelength>
<VRPTx:wt>1.0</VRPTx:wt>
</VRPTx:diffrn_radiation_wavelength>
</VRPTx:diffrn_radiation_wavelengthCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_radiation_wavelength.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_reflnType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_REFLN category record details about
the intensities in the diffraction data set
identified by attribute diffrn_id.
in category diffrn_refln
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in the particular diffraction
data set identified by attribute diffrn_id in category diffrn_reflns.
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4 for data set 'set1' reflection 1102.
<VRPTx:diffrn_reflnCategory>
<VRPTx:diffrn_refln diffrn_id="set1" id="1102">
<VRPTx:angle_chi>32.21</VRPTx:angle_chi>
<VRPTx:angle_kappa>20.12</VRPTx:angle_kappa>
<VRPTx:angle_omega>11.54</VRPTx:angle_omega>
<VRPTx:angle_phi>176.02</VRPTx:angle_phi>
<VRPTx:angle_psi>0.00</VRPTx:angle_psi>
<VRPTx:angle_theta>23.08</VRPTx:angle_theta>
<VRPTx:attenuator_code>Ni.005</VRPTx:attenuator_code>
<VRPTx:counts_bg_1>22</VRPTx:counts_bg_1>
<VRPTx:counts_bg_2>25</VRPTx:counts_bg_2>
<VRPTx:counts_net>3450</VRPTx:counts_net>
<VRPTx:counts_peak>321</VRPTx:counts_peak>
<VRPTx:counts_total>3499</VRPTx:counts_total>
<VRPTx:detect_slit_horiz>0.04</VRPTx:detect_slit_horiz>
<VRPTx:detect_slit_vert>0.02</VRPTx:detect_slit_vert>
<VRPTx:elapsed_time>1.00</VRPTx:elapsed_time>
<VRPTx:index_h>4</VRPTx:index_h>
<VRPTx:index_k>0</VRPTx:index_k>
<VRPTx:index_l>2</VRPTx:index_l>
<VRPTx:intensity_net>202.56</VRPTx:intensity_net>
<VRPTx:intensity_sigma>2.18</VRPTx:intensity_sigma>
<VRPTx:scale_group_code>A24</VRPTx:scale_group_code>
<VRPTx:scan_mode>om</VRPTx:scan_mode>
<VRPTx:scan_mode_backgd>mo</VRPTx:scan_mode_backgd>
<VRPTx:scan_rate>1.2</VRPTx:scan_rate>
<VRPTx:scan_time_backgd>900.00</VRPTx:scan_time_backgd>
<VRPTx:scan_width>1.0</VRPTx:scan_width>
<VRPTx:sint_over_lambda>0.25426</VRPTx:sint_over_lambda>
<VRPTx:standard_code>1</VRPTx:standard_code>
<VRPTx:wavelength>1.54184</VRPTx:wavelength>
<VRPTx:wavelength_id>Cu1fixed</VRPTx:wavelength_id>
</VRPTx:diffrn_refln>
</VRPTx:diffrn_reflnCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_refln.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_reflnsType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_REFLNS category record details about
the set of intensities measured in the diffraction experiment.
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in a diffraction data set.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_reflns.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_reflns_classType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_REFLNS_CLASS category record details
about the classes of reflections measured in the diffraction
experiment.
Example 1 - example corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~. Each reflection class is
defined by the number m=sum|m~i~|, where the m~i~ are the
integer coefficients that, in addition to h,k,l, index the
corresponding diffraction vector in the basis defined for
the reciprocal lattice.
<VRPTx:diffrn_reflns_classCategory>
<VRPTx:diffrn_reflns_class code="Main">
<VRPTx:av_R_eq>0.015</VRPTx:av_R_eq>
<VRPTx:d_res_high>0.551</VRPTx:d_res_high>
<VRPTx:d_res_low>6.136</VRPTx:d_res_low>
<VRPTx:description>m=0; main reflections</VRPTx:description>
<VRPTx:number>1580</VRPTx:number>
</VRPTx:diffrn_reflns_class>
<VRPTx:diffrn_reflns_class code="Sat1">
<VRPTx:av_R_eq>0.010</VRPTx:av_R_eq>
<VRPTx:d_res_high>0.551</VRPTx:d_res_high>
<VRPTx:d_res_low>6.136</VRPTx:d_res_low>
<VRPTx:description>m=1; first-order satellites</VRPTx:description>
<VRPTx:number>1045</VRPTx:number>
</VRPTx:diffrn_reflns_class>
</VRPTx:diffrn_reflns_classCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_reflns_class.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_scale_groupType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_SCALE_GROUP category record details
of the scaling factors applied to place all intensities in the
reflection lists on a common scale.
Scaling groups might, for example, correspond to each film in a
multi-film data set or each crystal in a multi-crystal data set.
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4.
<VRPTx:diffrn_scale_groupCategory>
<VRPTx:diffrn_scale_group code="A24">
<VRPTx:I_net>1.021</VRPTx:I_net>
</VRPTx:diffrn_scale_group>
</VRPTx:diffrn_scale_groupCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_scale_group.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_sourceType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_SOURCE category record details of
the source of radiation used in the diffraction experiment.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:diffrn_sourceCategory>
<VRPTx:diffrn_source diffrn_id="s1">
<VRPTx:current>180</VRPTx:current>
<VRPTx:power>50</VRPTx:power>
<VRPTx:size>8mm x 0.4 mm broad-focus</VRPTx:size>
<VRPTx:source>rotating anode</VRPTx:source>
<VRPTx:type>Rigaku RU-200</VRPTx:type>
</VRPTx:diffrn_source>
</VRPTx:diffrn_sourceCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_source.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_standard_reflnType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_STANDARD_REFLN category record details
about the reflections treated as standards during the measurement
of a set of diffraction intensities.
Note that these are the individual standard reflections, not the
results of the analysis of the standard reflections.
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<VRPTx:diffrn_standard_reflnCategory>
<VRPTx:diffrn_standard_refln code="1" diffrn_id="s1">
<VRPTx:index_h>3</VRPTx:index_h>
<VRPTx:index_k>2</VRPTx:index_k>
<VRPTx:index_l>4</VRPTx:index_l>
</VRPTx:diffrn_standard_refln>
<VRPTx:diffrn_standard_refln code="1" diffrn_id="s1">
<VRPTx:index_h>1</VRPTx:index_h>
<VRPTx:index_k>9</VRPTx:index_k>
<VRPTx:index_l>1</VRPTx:index_l>
</VRPTx:diffrn_standard_refln>
<VRPTx:diffrn_standard_refln code="1" diffrn_id="s1">
<VRPTx:index_h>3</VRPTx:index_h>
<VRPTx:index_k>0</VRPTx:index_k>
<VRPTx:index_l>10</VRPTx:index_l>
</VRPTx:diffrn_standard_refln>
</VRPTx:diffrn_standard_reflnCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_standard_refln.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | diffrn_standardsType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_STANDARDS category record details
about the set of standard reflections used to monitor intensity
stability during the measurement of diffraction intensities.
Note that these records describe properties common to the set of
standard reflections, not the standard reflections themselves.
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<VRPTx:diffrn_standardsCategory>
<VRPTx:diffrn_standards diffrn_id="s1">
<VRPTx:decay_>0</VRPTx:decay_>
<VRPTx:interval_time>120</VRPTx:interval_time>
<VRPTx:number>3</VRPTx:number>
</VRPTx:diffrn_standards>
</VRPTx:diffrn_standardsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/diffrn_standards.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_2d_crystal_entityType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_SYMMETRY_2DX category record
2D crystal symmetry parameters utilized in a 3DEM reconstruction.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_2d_crystal_entity.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_3d_crystal_entityType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_SYMMETRY_3DX category record
3D crystal symmetry parameters utilized in 3DEM reconstruction averaging.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_3d_crystal_entity.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_3d_fittingType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the 3D_FITTING category
record details of the method of fitting atomic
coordinates from a PDB file into a 3d-em
volume map file
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<VRPTx:em_3d_fittingCategory>
<VRPTx:em_3d_fitting entry_id="1DYL" id="1">
<VRPTx:details> THE CRYSTAL STRUCTURE OF THE CAPSID
PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359
(SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM
DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED
INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE
FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET
OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED
BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT
(CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT
CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563
ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE
AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5
SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222
ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN
DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE
PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS
GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER
OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY
THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE
DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE
MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE
ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE
HIGHEST PSEUDO TEMPERATURE FACTORS.</VRPTx:details>
<VRPTx:method>AUTOMATIC</VRPTx:method>
<VRPTx:overall_b_value xsi:nil="true" />
<VRPTx:ref_protocol>RIGID BODY REFINEMENT</VRPTx:ref_protocol>
<VRPTx:ref_space>REAL</VRPTx:ref_space>
<VRPTx:target_criteria>R-FACTOR</VRPTx:target_criteria>
</VRPTx:em_3d_fitting>
</VRPTx:em_3d_fittingCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_3d_fitting.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_3d_fitting_listType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the 3D_FITTING_LIST category
lists the methods of fitting atomic coordinates from a PDB file
into a 3d-em volume map file
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<VRPTx:em_3d_fitting_listCategory>
<VRPTx:em_3d_fitting_list _3d_fitting_id="l" id="1">
<VRPTx:pdb_chain_id xsi:nil="true" />
<VRPTx:pdb_entry_id>1VCQ</VRPTx:pdb_entry_id>
</VRPTx:em_3d_fitting_list>
</VRPTx:em_3d_fitting_listCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_3d_fitting_list.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_3d_reconstructionType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_3D_RECONSTRUCTION category
record details of the 3D reconstruction procedure from 2D projections.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<VRPTx:em_3d_reconstructionCategory>
<VRPTx:em_3d_reconstruction id="1">
<VRPTx:actual_pixel_size>2.52</VRPTx:actual_pixel_size>
<VRPTx:details xsi:nil="true" />
<VRPTx:entry_id>1DYL</VRPTx:entry_id>
<VRPTx:method>CROSS-COMMON LINES</VRPTx:method>
<VRPTx:nominal_pixel_size>2.64</VRPTx:nominal_pixel_size>
<VRPTx:resolution>9</VRPTx:resolution>
<VRPTx:resolution_method xsi:nil="true" />
</VRPTx:em_3d_reconstruction>
</VRPTx:em_3d_reconstructionCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_3d_reconstruction.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_adminType |
|---|---|
| Abstract | no |
| Documentation |
Administration-related data items
Example 1
<VRPTx:em_adminCategory>
<VRPTx:em_admin entry_id="D_100005">
<VRPTx:current_status>REL</VRPTx:current_status>
<VRPTx:deposition_date>2008-12-01</VRPTx:deposition_date>
<VRPTx:details xsi:nil="true" />
<VRPTx:last_update>2011-05-22</VRPTx:last_update>
<VRPTx:map_release_date>2009-12-01</VRPTx:map_release_date>
</VRPTx:em_admin>
</VRPTx:em_adminCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_admin.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_bufferType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the BUFFER category
record details of the sample buffer.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_buffer.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_buffer_componentType |
|---|---|
| Abstract | no |
| Documentation |
Buffer category
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_buffer_component.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_crystal_formationType |
|---|---|
| Abstract | no |
| Documentation |
Description of growth of a 2D, 3D, or helical crystal array.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_crystal_formation.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_ctf_correctionType |
|---|---|
| Abstract | no |
| Documentation |
Description of the Contrast Transfer Function (CTF) correction
Example 1 -
<VRPTx:em_ctf_correctionCategory>
<VRPTx:em_ctf_correction id="1">
<VRPTx:em_image_processing_id>1</VRPTx:em_image_processing_id>
<VRPTx:type>PHASE FLIPPING ONLY</VRPTx:type>
</VRPTx:em_ctf_correction>
</VRPTx:em_ctf_correctionCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_ctf_correction.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_diffractionType |
|---|---|
| Abstract | no |
| Documentation |
Microscopy parameters relevant only for crystallography
Example 1 -
<VRPTx:em_diffractionCategory>
<VRPTx:em_diffraction id="1">
<VRPTx:camera_length>800</VRPTx:camera_length>
<VRPTx:imaging_id>1</VRPTx:imaging_id>
</VRPTx:em_diffraction>
<VRPTx:em_diffraction id="2">
<VRPTx:camera_length>750</VRPTx:camera_length>
<VRPTx:imaging_id>2</VRPTx:imaging_id>
</VRPTx:em_diffraction>
</VRPTx:em_diffractionCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_diffraction.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_diffraction_shellType |
|---|---|
| Abstract | no |
| Documentation |
Statistical parameters for electron diffraction measurements
within a resolution shell
Example 1 -
<VRPTx:em_diffraction_shellCategory>
<VRPTx:em_diffraction_shell id="1">
<VRPTx:fourier_space_coverage>93.0</VRPTx:fourier_space_coverage>
<VRPTx:high_resolution>7.5</VRPTx:high_resolution>
<VRPTx:low_resolution>45</VRPTx:low_resolution>
<VRPTx:multiplicity>2.3</VRPTx:multiplicity>
<VRPTx:num_structure_factors>327</VRPTx:num_structure_factors>
<VRPTx:phase_residual>13.5</VRPTx:phase_residual>
</VRPTx:em_diffraction_shell>
</VRPTx:em_diffraction_shellCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_diffraction_shell.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_diffraction_statsType |
|---|---|
| Abstract | no |
| Documentation |
Statistical parameters for electron diffraction measurements
Example 1 -
<VRPTx:em_diffraction_statsCategory>
<VRPTx:em_diffraction_stats id="1">
<VRPTx:fourier_space_coverage>92</VRPTx:fourier_space_coverage>
<VRPTx:high_resolution>7.2</VRPTx:high_resolution>
<VRPTx:num_intensities_measured>1524</VRPTx:num_intensities_measured>
<VRPTx:num_structure_factors>325</VRPTx:num_structure_factors>
<VRPTx:overall_phase_error>18.6</VRPTx:overall_phase_error>
<VRPTx:overall_phase_residual>9.5</VRPTx:overall_phase_residual>
<VRPTx:phase_error_rejection_criteria>None</VRPTx:phase_error_rejection_criteria>
<VRPTx:r_merge>19.5</VRPTx:r_merge>
<VRPTx:r_sym>23.2</VRPTx:r_sym>
</VRPTx:em_diffraction_stats>
</VRPTx:em_diffraction_statsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_diffraction_stats.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_embeddingType |
|---|---|
| Abstract | no |
| Documentation |
Sugar embedding category
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_embedding.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_entity_assemblyType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_ENTITY_ASSEMBLY category
record details about each component of
the complex.
Example 1 - based on PDB entry 1C2W
<VRPTx:em_entity_assemblyCategory>
<VRPTx:em_entity_assembly id="1">
<VRPTx:name>50S Ribosomal Subunit</VRPTx:name>
<VRPTx:parent_id>0</VRPTx:parent_id>
<VRPTx:type>RIBOSOME</VRPTx:type>
</VRPTx:em_entity_assembly>
</VRPTx:em_entity_assemblyCategory>
Example 2 - based on PDB entry 3IY7
<VRPTx:em_entity_assemblyCategory>
<VRPTx:em_entity_assembly id="1">
<VRPTx:name>Fab fragment from MAb F interacting with feline panleukopenia virus (FPV)</VRPTx:name>
<VRPTx:parent_id>0</VRPTx:parent_id>
<VRPTx:type>COMPLEX</VRPTx:type>
</VRPTx:em_entity_assembly>
<VRPTx:em_entity_assembly id="2">
<VRPTx:name>feline panleukopenia virus</VRPTx:name>
<VRPTx:parent_id>1</VRPTx:parent_id>
<VRPTx:synonym>FPV</VRPTx:synonym>
<VRPTx:type>VIRUS</VRPTx:type>
</VRPTx:em_entity_assembly>
<VRPTx:em_entity_assembly id="3">
<VRPTx:name>Fab fragment from Mab F</VRPTx:name>
<VRPTx:parent_id>1</VRPTx:parent_id>
<VRPTx:synonym>Fab</VRPTx:synonym>
<VRPTx:type>COMPLEX</VRPTx:type>
</VRPTx:em_entity_assembly>
</VRPTx:em_entity_assemblyCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_entity_assembly.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_entity_assembly_molwtType |
|---|---|
| Abstract | no |
| Documentation |
Data items in this category record details about the molecular weight of
an assembly component of the sample.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<VRPTx:em_entity_assembly_molwtCategory>
<VRPTx:em_entity_assembly_molwt entity_assembly_id="1" id="1">
<VRPTx:units>MEGADALTONS</VRPTx:units>
<VRPTx:value>30.5</VRPTx:value>
</VRPTx:em_entity_assembly_molwt>
</VRPTx:em_entity_assembly_molwtCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_entity_assembly_molwt.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_entity_assembly_naturalsourceType |
|---|---|
| Abstract | no |
| Documentation |
Data items in this category record taxonomic details about the natural source for EM
assemblies and assembly components.
Example 1 -
<VRPTx:em_entity_assembly_naturalsourceCategory>
<VRPTx:em_entity_assembly_naturalsource entity_assembly_id="8333" id="1">
<VRPTx:cellular_location xsi:nil="true" />
<VRPTx:ncbi_tax_id>Escherichia coli</VRPTx:ncbi_tax_id>
<VRPTx:organ xsi:nil="true" />
<VRPTx:organelle>cytoplasm</VRPTx:organelle>
<VRPTx:organism>K12</VRPTx:organism>
<VRPTx:strain xsi:nil="true" />
<VRPTx:tissue xsi:nil="true" />
</VRPTx:em_entity_assembly_naturalsource>
</VRPTx:em_entity_assembly_naturalsourceCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_entity_assembly_naturalsource.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_entity_assembly_recombinantType |
|---|---|
| Abstract | no |
| Documentation |
Data items in this category record details
about recombinant expression of the assembly or assembly component.
Example 1 -
<VRPTx:em_entity_assembly_recombinantCategory>
<VRPTx:em_entity_assembly_recombinant entity_assembly_id="1" id="1">
<VRPTx:organism>Escherichia coli</VRPTx:organism>
<VRPTx:plasmid>pET17c</VRPTx:plasmid>
</VRPTx:em_entity_assembly_recombinant>
</VRPTx:em_entity_assembly_recombinantCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_entity_assembly_recombinant.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_entity_assembly_syntheticType |
|---|---|
| Abstract | no |
| Documentation |
Data items in this category record taxonomic details about the synthetic source for EM
assemblies and assembly components.
Example 1
<VRPTx:em_entity_assembly_syntheticCategory>
<VRPTx:em_entity_assembly_synthetic entity_assembly_id="1" id="1">
<VRPTx:cellular_location xsi:nil="true" />
<VRPTx:ncbi_tax_id>8333</VRPTx:ncbi_tax_id>
<VRPTx:organ xsi:nil="true" />
<VRPTx:organelle xsi:nil="true" />
<VRPTx:organism>Escherichia coli</VRPTx:organism>
<VRPTx:strain>K12</VRPTx:strain>
<VRPTx:tissue xsi:nil="true" />
</VRPTx:em_entity_assembly_synthetic>
</VRPTx:em_entity_assembly_syntheticCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_entity_assembly_synthetic.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_experimentType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_EXPERIMENT category provide
high-level classification of the EM experiment.
Example 1 - based on PDB entry 1EG0
<VRPTx:em_experimentCategory>
<VRPTx:em_experiment entry_id="1EG0">
<VRPTx:aggregation_state>PARTICLE</VRPTx:aggregation_state>
<VRPTx:reconstruction_method>SINGLE PARTICLE</VRPTx:reconstruction_method>
</VRPTx:em_experiment>
</VRPTx:em_experimentCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_experiment.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_helical_entityType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_HELICAL_ENTITY category record details
for a helical or filament type of assembly component.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_helical_entity.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_image_processingType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_IMAGE_PROCESSING category
record details of the EM image processing procedure.
Example 1 -
<VRPTx:em_image_processingCategory>
<VRPTx:em_image_processing id="1" image_recording_id="1">
<VRPTx:details>The selected images were high-pass filtered and normalized</VRPTx:details>
</VRPTx:em_image_processing>
</VRPTx:em_image_processingCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_image_processing.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_image_recordingType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_IMAGE_RECORDING category record details
of the image recording (either film/microdensitometer or electronic detector)
and parameters for image digitization.
Example 1 - images collected on film
<VRPTx:em_image_recordingCategory>
<VRPTx:em_image_recording id="1" imaging_id="1">
<VRPTx:avg_electron_dose_per_image>0.9</VRPTx:avg_electron_dose_per_image>
<VRPTx:film_or_detector_model>GENERIC FILM</VRPTx:film_or_detector_model>
<VRPTx:num_diffraction_images>48</VRPTx:num_diffraction_images>
</VRPTx:em_image_recording>
</VRPTx:em_image_recordingCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_image_recording.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_image_scansType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_IMAGE_SCANS category record details
of the image scanning device (microdensitometer)
and parameters for digitization of the image.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<VRPTx:em_image_scansCategory>
<VRPTx:em_image_scans id="2">
<VRPTx:details xsi:nil="true" />
<VRPTx:entry_id>1DYL</VRPTx:entry_id>
<VRPTx:number_digital_images>48</VRPTx:number_digital_images>
<VRPTx:od_range xsi:nil="true" />
<VRPTx:quant_bit_size xsi:nil="true" />
<VRPTx:sampling_size xsi:nil="true" />
<VRPTx:scanner_model xsi:nil="true" />
</VRPTx:em_image_scans>
</VRPTx:em_image_scansCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_image_scans.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_imagingType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_IMAGING category record details about
the parameters used in imaging the sample in the electron microscope.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<VRPTx:em_imagingCategory>
<VRPTx:em_imaging entry_id="1DYL" id="1">
<VRPTx:accelerating_voltage>200</VRPTx:accelerating_voltage>
<VRPTx:calibrated_magnification xsi:nil="true" />
<VRPTx:date>1998-15-06</VRPTx:date>
<VRPTx:details xsi:nil="true" />
<VRPTx:detector_distance xsi:nil="true" />
<VRPTx:electron_source>FEG</VRPTx:electron_source>
<VRPTx:illumination_mode>bright field</VRPTx:illumination_mode>
<VRPTx:microscope_model>FEI/PHILIPS CM200 FEG</VRPTx:microscope_model>
<VRPTx:mode>low dose</VRPTx:mode>
<VRPTx:nominal_cs>2.0</VRPTx:nominal_cs>
<VRPTx:nominal_defocus_max>7600</VRPTx:nominal_defocus_max>
<VRPTx:nominal_defocus_min>975</VRPTx:nominal_defocus_min>
<VRPTx:nominal_magnification>50000</VRPTx:nominal_magnification>
<VRPTx:recording_temperature_maximum xsi:nil="true" />
<VRPTx:recording_temperature_minimum xsi:nil="true" />
<VRPTx:specimen_holder_model>gatan 626-0300</VRPTx:specimen_holder_model>
<VRPTx:specimen_holder_type>cryotransfer</VRPTx:specimen_holder_type>
<VRPTx:temperature>95</VRPTx:temperature>
<VRPTx:tilt_angle_max>0</VRPTx:tilt_angle_max>
<VRPTx:tilt_angle_min>0</VRPTx:tilt_angle_min>
</VRPTx:em_imaging>
</VRPTx:em_imagingCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_imaging.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_imaging_opticsType |
|---|---|
| Abstract | no |
| Documentation |
Description of a few specialist optics apparatus
Example 1 -
<VRPTx:em_imaging_opticsCategory>
<VRPTx:em_imaging_optics id="1" imaging_id="1">
<VRPTx:chr_aberration_corrector>CEOS manufactured Cc corrector</VRPTx:chr_aberration_corrector>
<VRPTx:energyfilter_lower>0</VRPTx:energyfilter_lower>
<VRPTx:energyfilter_name>FEI</VRPTx:energyfilter_name>
<VRPTx:energyfilter_upper>15</VRPTx:energyfilter_upper>
</VRPTx:em_imaging_optics>
</VRPTx:em_imaging_opticsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_imaging_optics.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_particle_selectionType |
|---|---|
| Abstract | no |
| Documentation |
Data items in this category
record details of images from scanned micrographs and the
number of particles selected from a scanned set of micrographs.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<VRPTx:em_particle_selectionCategory>
<VRPTx:em_particle_selection id="1" image_processing_id="1">
<VRPTx:details xsi:nil="true" />
<VRPTx:method>INTERACTIVE</VRPTx:method>
<VRPTx:num_particles_selected>5267</VRPTx:num_particles_selected>
</VRPTx:em_particle_selection>
</VRPTx:em_particle_selectionCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_particle_selection.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_single_particle_entityType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_SINGLE_PARTICLE_ENTITY category provide
the details of the symmetry for a single particle entity type.
Example 1 -
<VRPTx:em_single_particle_entityCategory>
<VRPTx:em_single_particle_entity id="1" image_processing_id="1">
<VRPTx:point_symmetry>I</VRPTx:point_symmetry>
</VRPTx:em_single_particle_entity>
</VRPTx:em_single_particle_entityCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_single_particle_entity.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_softwareType |
|---|---|
| Abstract | no |
| Documentation |
Description of the software that was used for data collection, data processing,
data analysis, structure calculations and refinement. The description should
include the name of the software, the author of the software and the version used.
Example 1 -
<VRPTx:em_softwareCategory>
<VRPTx:em_software id="1">
<VRPTx:category>IMAGE ACQUISITION</VRPTx:category>
<VRPTx:details xsi:nil="true" />
<VRPTx:name>Leginon</VRPTx:name>
<VRPTx:version>1.3</VRPTx:version>
</VRPTx:em_software>
<VRPTx:em_software id="2">
<VRPTx:category>PARTICLE SELECTION</VRPTx:category>
<VRPTx:details xsi:nil="true" />
<VRPTx:name>X3D</VRPTx:name>
<VRPTx:version xsi:nil="true" />
</VRPTx:em_software>
<VRPTx:em_software id="3">
<VRPTx:category>BACKGROUND MASKING</VRPTx:category>
<VRPTx:details xsi:nil="true" />
<VRPTx:name>bsoft</VRPTx:name>
<VRPTx:version>1.1</VRPTx:version>
</VRPTx:em_software>
<VRPTx:em_software id="4">
<VRPTx:category>RECONSTRUCTION</VRPTx:category>
<VRPTx:details>em3dr2 -low 20</VRPTx:details>
<VRPTx:name>EM2DR2</VRPTx:name>
<VRPTx:version>3.2</VRPTx:version>
</VRPTx:em_software>
<VRPTx:em_software id="5">
<VRPTx:category>EULER ASSIGNMENT</VRPTx:category>
<VRPTx:details xsi:nil="true" />
<VRPTx:name>erandom</VRPTx:name>
<VRPTx:version xsi:nil="true" />
</VRPTx:em_software>
<VRPTx:em_software id="6">
<VRPTx:category>CTF CORRECTION</VRPTx:category>
<VRPTx:details xsi:nil="true" />
<VRPTx:name>bctf</VRPTx:name>
<VRPTx:version xsi:nil="true" />
</VRPTx:em_software>
<VRPTx:em_software id="7">
<VRPTx:category>MODEL FITTING</VRPTx:category>
<VRPTx:details xsi:nil="true" />
<VRPTx:name>chimera</VRPTx:name>
<VRPTx:version>1.6</VRPTx:version>
</VRPTx:em_software>
</VRPTx:em_softwareCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_software.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_specimenType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EMD_SPECIMEN category record details
about specimens prepared for imaging by electron microscopy.
Example 1 - based on PDB 2FL8
<VRPTx:em_specimenCategory>
<VRPTx:em_specimen experiment_id="1" id="1">
<VRPTx:embedding_applied>NO</VRPTx:embedding_applied>
<VRPTx:shadowing_applied>NO</VRPTx:shadowing_applied>
<VRPTx:staining_applied>NO</VRPTx:staining_applied>
<VRPTx:vitrification_applied>YES</VRPTx:vitrification_applied>
</VRPTx:em_specimen>
</VRPTx:em_specimenCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_specimen.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_stainingType |
|---|---|
| Abstract | no |
| Documentation |
Staining category
Example 1 -
<VRPTx:em_stainingCategory>
<VRPTx:em_staining id="1">
<VRPTx:material>Uranyl Acetate</VRPTx:material>
<VRPTx:specimen_id>1</VRPTx:specimen_id>
<VRPTx:type>NEGATIVE</VRPTx:type>
</VRPTx:em_staining>
</VRPTx:em_stainingCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_staining.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_virus_entityType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_VIRUS_ENTITY category record details
of the icosahedral virus.
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<VRPTx:em_virus_entityCategory>
<VRPTx:em_virus_entity entity_assembly_id="1" id="1">
<VRPTx:empty>NO</VRPTx:empty>
<VRPTx:enveloped>YES</VRPTx:enveloped>
<VRPTx:virus_host_category>VERTERBRATES</VRPTx:virus_host_category>
<VRPTx:virus_isolate>STRAIN</VRPTx:virus_isolate>
<VRPTx:virus_type>VIRUS</VRPTx:virus_type>
</VRPTx:em_virus_entity>
</VRPTx:em_virus_entityCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_virus_entity.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_virus_natural_hostType |
|---|---|
| Abstract | no |
| Documentation |
Data items in this category record details of a virus entity.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_virus_natural_host.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_virus_shellType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EMD_VIRUS_SHELL category record details
of the viral shell number, shell diameter, and icosahedral triangulation number.
Example 1 - Bluetongue Virus
<VRPTx:em_virus_shellCategory>
<VRPTx:em_virus_shell entity_assembly_id="1" id="1">
<VRPTx:diameter>348</VRPTx:diameter>
<VRPTx:name>VP7 layer</VRPTx:name>
<VRPTx:triangulation>13</VRPTx:triangulation>
</VRPTx:em_virus_shell>
<VRPTx:em_virus_shell entity_assembly_id="1" id="2">
<VRPTx:diameter>348</VRPTx:diameter>
<VRPTx:name>VP3 layer</VRPTx:name>
<VRPTx:triangulation>2</VRPTx:triangulation>
</VRPTx:em_virus_shell>
</VRPTx:em_virus_shellCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_virus_shell.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_virus_syntheticType |
|---|---|
| Abstract | no |
| Documentation |
Data items in this category record details of a synthetic virus entity.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_virus_synthetic.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_vitrificationType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EM_VITRIFICATION category
record details about the method and cryogen used in
rapid freezing of the sample on the grid prior to its
insertion in the electron microscope
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<VRPTx:em_vitrificationCategory>
<VRPTx:em_vitrification id="1">
<VRPTx:cryogen_name>ETHANE</VRPTx:cryogen_name>
<VRPTx:details> SAMPLES WERE PREPARED AS THIN
LAYERS OF VITREOUS ICE AND
MAINTAINED AT NEAR LIQUID NITROGEN
TEMPERATURE IN THE ELECTRON MICROSCOPE
WITH A GATAN 626-0300 CRYOTRANSFER
HOLDER.</VRPTx:details>
<VRPTx:entry_id>1DYL</VRPTx:entry_id>
<VRPTx:humidity>90</VRPTx:humidity>
<VRPTx:instrument xsi:nil="true" />
<VRPTx:method>PLUNGE VITRIFICATION</VRPTx:method>
<VRPTx:temp>95</VRPTx:temp>
<VRPTx:time_resolved_state xsi:nil="true" />
</VRPTx:em_vitrification>
</VRPTx:em_vitrificationCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_vitrification.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | em_volume_selectionType |
|---|---|
| Abstract | no |
| Documentation |
Volume selection in image processing
Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
<VRPTx:em_volume_selectionCategory>
<VRPTx:em_volume_selection id="1" image_processing_id="1">
<VRPTx:details xsi:nil="true" />
<VRPTx:method>INTERACTIVE</VRPTx:method>
<VRPTx:num_volumes_extracted>5267</VRPTx:num_volumes_extracted>
</VRPTx:em_volume_selection>
</VRPTx:em_volume_selectionCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/em_volume_selection.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | entityType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the ENTITY category record details (such as
chemical composition, name and source) about the molecular
entities that are present in the crystallographic structure.
Items in the various ENTITY subcategories provide a full
chemical description of these molecular entities.
Entities are of three types: polymer, non-polymer and water.
Note that the water category includes only water; ordered
solvent such as sulfate ion or acetone would be described as
individual non-polymer entities.
The ENTITY category is specific to macromolecular CIF
applications and replaces the function of the CHEMICAL category
in the CIF core.
It is important to remember that the ENTITY data are not the
result of the crystallographic experiment; those results are
represented by the ATOM_SITE data items. ENTITY data items
describe the chemistry of the molecules under investigation
and can most usefully be thought of as the ideal groups to which
the structure is restrained or constrained during refinement.
It is also important to remember that entities do not correspond
directly to the enumeration of the contents of the asymmetric
unit. Entities are described only once, even in those structures
that contain multiple observations of an entity. The
STRUCT_ASYM data items, which reference the entity list,
describe and label the contents of the asymmetric unit.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:entityCategory>
<VRPTx:entity id="1">
<VRPTx:details> The enzymatically competent form of HIV
protease is a dimer. This entity
corresponds to one monomer of an active dimer.</VRPTx:details>
<VRPTx:formula_weight>10916</VRPTx:formula_weight>
<VRPTx:type>polymer</VRPTx:type>
</VRPTx:entity>
<VRPTx:entity id="2">
<VRPTx:details xsi:nil="true" />
<VRPTx:formula_weight>762</VRPTx:formula_weight>
<VRPTx:type>non-polymer</VRPTx:type>
</VRPTx:entity>
<VRPTx:entity id="3">
<VRPTx:details xsi:nil="true" />
<VRPTx:formula_weight>18</VRPTx:formula_weight>
<VRPTx:type>water</VRPTx:type>
</VRPTx:entity>
</VRPTx:entityCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entity.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | entity_name_comType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the ENTITY_NAME_COM category record the common name
or names associated with the entity. In some cases, the entity
name may not be the same as the name of the biological structure.
For example, haemoglobin alpha chain would be the entity common
name, not haemoglobin.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:entity_name_comCategory>
<VRPTx:entity_name_com entity_id="1">
<VRPTx:name>HIV-1 protease monomer</VRPTx:name>
</VRPTx:entity_name_com>
<VRPTx:entity_name_com entity_id="1">
<VRPTx:name>HIV-1 PR monomer</VRPTx:name>
</VRPTx:entity_name_com>
<VRPTx:entity_name_com entity_id="2">
<VRPTx:name>acetyl-pepstatin</VRPTx:name>
</VRPTx:entity_name_com>
<VRPTx:entity_name_com entity_id="2">
<VRPTx:name>acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine</VRPTx:name>
</VRPTx:entity_name_com>
<VRPTx:entity_name_com entity_id="3">
<VRPTx:name>water</VRPTx:name>
</VRPTx:entity_name_com>
</VRPTx:entity_name_comCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entity_name_com.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | entity_name_sysType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the ENTITY_NAME_SYS category record the systematic
name or names associated with the entity and the system that
was used to construct the systematic name. In some cases, the
entity name may not be the same as the name of the biological
structure.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:entity_name_sysCategory>
<VRPTx:entity_name_sys entity_id="1">
<VRPTx:name>EC 3.4.23.16</VRPTx:name>
</VRPTx:entity_name_sys>
<VRPTx:entity_name_sys entity_id="2">
<VRPTx:name>acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta</VRPTx:name>
</VRPTx:entity_name_sys>
<VRPTx:entity_name_sys entity_id="3">
<VRPTx:name>water</VRPTx:name>
</VRPTx:entity_name_sys>
</VRPTx:entity_name_sysCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entity_name_sys.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | entity_polyType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the ENTITY_POLY category record details about the
polymer, such as the type of the polymer, the number of
monomers and whether it has nonstandard features.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:entity_polyCategory>
<VRPTx:entity_poly entity_id="1">
<VRPTx:nstd_chirality>no</VRPTx:nstd_chirality>
<VRPTx:nstd_linkage>no</VRPTx:nstd_linkage>
<VRPTx:nstd_monomer>no</VRPTx:nstd_monomer>
<VRPTx:type>polypeptide(L)</VRPTx:type>
<VRPTx:type_details xsi:nil="true" />
</VRPTx:entity_poly>
</VRPTx:entity_polyCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entity_poly.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | entity_poly_seqType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the ENTITY_POLY_SEQ category specify the sequence
of monomers in a polymer. Allowance is made for the possibility
of microheterogeneity in a sample by allowing a given sequence
number to be correlated with more than one monomer ID. The
corresponding ATOM_SITE entries should reflect this
heterogeneity.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:entity_poly_seqCategory>
<VRPTx:entity_poly_seq entity_id="1" mon_id="PRO" num="1"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="GLN" num="2"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="ILE" num="3"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="THR" num="4"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="LEU" num="5"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="TRP" num="6"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="GLN" num="7"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="ARG" num="8"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="PRO" num="9"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="LEU" num="10"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="VAL" num="11"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="THR" num="12"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="ILE" num="13"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="LYS" num="14"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="ILE" num="15"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="GLY" num="16"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="GLY" num="17"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="GLN" num="18"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="LEU" num="19"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="LYS" num="20"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="GLU" num="21"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="ALA" num="22"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="LEU" num="23"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="LEU" num="24"></VRPTx:entity_poly_seq>
<VRPTx:entity_poly_seq entity_id="1" mon_id="ASP" num="25"></VRPTx:entity_poly_seq>
</VRPTx:entity_poly_seqCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entity_poly_seq.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | entryType |
|---|---|
| Abstract | no |
| Documentation |
There is only one item in the ENTRY category, attribute id in category entry. This
data item gives a name to this entry and is indirectly a key to
the categories (such as CELL, GEOM, EXPTL) that describe
information pertinent to the entire data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:entryCategory>
<VRPTx:entry id="5HVP"></VRPTx:entry>
</VRPTx:entryCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<VRPTx:entryCategory>
<VRPTx:entry id="TOZ"></VRPTx:entry>
</VRPTx:entryCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entry.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | entry_linkType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the ENTRY_LINK category record the
relationships between the current data block
identified by attribute id in category entry and other data blocks
within the current file which may be referenced
in the current data block.
Example 1 - example file for the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
<VRPTx:entry_linkCategory>
<VRPTx:entry_link entry_id="KSE_TEXT" id="KSE_COM">
<VRPTx:details>experimental data common to ref./mod. structures</VRPTx:details>
</VRPTx:entry_link>
<VRPTx:entry_link entry_id="KSE_TEXT" id="KSE_REF">
<VRPTx:details>reference structure</VRPTx:details>
</VRPTx:entry_link>
<VRPTx:entry_link entry_id="KSE_TEXT" id="KSE_MOD">
<VRPTx:details>modulated structure</VRPTx:details>
</VRPTx:entry_link>
</VRPTx:entry_linkCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entry_link.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | exptlType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the EXPTL category record details about the
experimental work prior to the intensity measurements and
details about the absorption-correction technique employed.
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4.
<VRPTx:exptlCategory>
<VRPTx:exptl entry_id="datablock1" method="single-crystal x-ray diffraction">
<VRPTx:absorpt_coefficient_mu>1.22</VRPTx:absorpt_coefficient_mu>
<VRPTx:absorpt_correction_T_max>0.896</VRPTx:absorpt_correction_T_max>
<VRPTx:absorpt_correction_T_min>0.802</VRPTx:absorpt_correction_T_min>
<VRPTx:absorpt_correction_type>integration</VRPTx:absorpt_correction_type>
<VRPTx:absorpt_process_details> Gaussian grid method from SHELX76
Sheldrick, G. M., "SHELX-76: structure determination and
refinement program", Cambridge University, UK, 1976</VRPTx:absorpt_process_details>
<VRPTx:crystals_number>1</VRPTx:crystals_number>
<VRPTx:details> Enraf-Nonius LT2 liquid nitrogen variable-temperature
device used</VRPTx:details>
<VRPTx:method_details> graphite monochromatized Cu K(alpha) fixed tube and
Enraf-Nonius CAD4 diffractometer used</VRPTx:method_details>
</VRPTx:exptl>
</VRPTx:exptlCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/exptl.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | ndb_struct_conf_naType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the NDB_STRUCT_CONF_NA category
describes secondary structure features in this entry.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/ndb_struct_conf_na.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | ndb_struct_na_base_pairType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the NDB_STRUCT_NA_BASE_PAIR category record details
of base pairing interactions.
<VRPTx:ndb_struct_na_base_pairCategory>
<VRPTx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="1" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="8" j_symmetry="7_555" model_number="1">
<VRPTx:buckle>-5.523</VRPTx:buckle>
<VRPTx:opening>-3.291</VRPTx:opening>
<VRPTx:propeller>-6.752</VRPTx:propeller>
<VRPTx:shear>-0.396</VRPTx:shear>
<VRPTx:stagger>-0.018</VRPTx:stagger>
<VRPTx:stretch>-0.156</VRPTx:stretch>
</VRPTx:ndb_struct_na_base_pair>
<VRPTx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="2" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="7" j_symmetry="7_555" model_number="1">
<VRPTx:buckle>-4.727</VRPTx:buckle>
<VRPTx:opening>2.311</VRPTx:opening>
<VRPTx:propeller>-9.765</VRPTx:propeller>
<VRPTx:shear>-0.094</VRPTx:shear>
<VRPTx:stagger>-0.334</VRPTx:stagger>
<VRPTx:stretch>-0.220</VRPTx:stretch>
</VRPTx:ndb_struct_na_base_pair>
<VRPTx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="3" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="6" j_symmetry="7_555" model_number="1">
<VRPTx:buckle>-6.454</VRPTx:buckle>
<VRPTx:opening>-1.181</VRPTx:opening>
<VRPTx:propeller>-12.575</VRPTx:propeller>
<VRPTx:shear>-0.285</VRPTx:shear>
<VRPTx:stagger>0.008</VRPTx:stagger>
<VRPTx:stretch>-0.239</VRPTx:stretch>
</VRPTx:ndb_struct_na_base_pair>
</VRPTx:ndb_struct_na_base_pairCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/ndb_struct_na_base_pair.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | ndb_struct_na_base_pair_stepType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details
of base pair step interactions.
<VRPTx:ndb_struct_na_base_pair_stepCategory>
<VRPTx:ndb_struct_na_base_pair_step i_label_asym_id_1="A" i_label_asym_id_2="A" i_label_comp_id_1="G" i_label_comp_id_2="G" i_label_seq_id_1="1" i_label_seq_id_2="2" i_symmetry_1="1_555" i_symmetry_2="1_555" j_label_asym_id_1="A" j_label_asym_id_2="A" j_label_comp_id_1="C" j_label_comp_id_2="C" j_label_seq_id_1="8" j_label_seq_id_2="7" j_symmetry_1="7_555" j_symmetry_2="7_555" model_number="1">
<VRPTx:rise>3.339</VRPTx:rise>
<VRPTx:roll>9.755</VRPTx:roll>
<VRPTx:shift>0.369</VRPTx:shift>
<VRPTx:slide>-1.414</VRPTx:slide>
<VRPTx:tilt>3.056</VRPTx:tilt>
<VRPTx:twist>33.530</VRPTx:twist>
</VRPTx:ndb_struct_na_base_pair_step>
<VRPTx:ndb_struct_na_base_pair_step i_label_asym_id_1="A" i_label_asym_id_2="A" i_label_comp_id_1="G" i_label_comp_id_2="G" i_label_seq_id_1="2" i_label_seq_id_2="3" i_symmetry_1="1_555" i_symmetry_2="1_555" j_label_asym_id_1="A" j_label_asym_id_2="A" j_label_comp_id_1="C" j_label_comp_id_2="C" j_label_seq_id_1="7" j_label_seq_id_2="6" j_symmetry_1="7_555" j_symmetry_2="7_555" model_number="1">
<VRPTx:rise>3.371</VRPTx:rise>
<VRPTx:roll>6.725</VRPTx:roll>
<VRPTx:shift>0.176</VRPTx:shift>
<VRPTx:slide>-1.672</VRPTx:slide>
<VRPTx:tilt>-1.176</VRPTx:tilt>
<VRPTx:twist>30.004</VRPTx:twist>
</VRPTx:ndb_struct_na_base_pair_step>
</VRPTx:ndb_struct_na_base_pair_stepCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/ndb_struct_na_base_pair_step.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_audit_authorType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_AUDIT_AUTHOR category record details about
the author(s) of the data block.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
<VRPTx:pdbx_audit_authorCategory>
<VRPTx:pdbx_audit_author ordinal="1">
<VRPTx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</VRPTx:address>
<VRPTx:name>Fitzgerald, Paula M.D.</VRPTx:name>
</VRPTx:pdbx_audit_author>
<VRPTx:pdbx_audit_author ordinal="2">
<VRPTx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</VRPTx:address>
<VRPTx:name>McKeever, Brian M.</VRPTx:name>
</VRPTx:pdbx_audit_author>
<VRPTx:pdbx_audit_author ordinal="3">
<VRPTx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</VRPTx:address>
<VRPTx:name>Van Middlesworth, J.F.</VRPTx:name>
</VRPTx:pdbx_audit_author>
<VRPTx:pdbx_audit_author ordinal="4">
<VRPTx:address> Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA</VRPTx:address>
<VRPTx:name>Springer, James P.</VRPTx:name>
</VRPTx:pdbx_audit_author>
</VRPTx:pdbx_audit_authorCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_audit_author.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_audit_revision_categoryType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_AUDIT_REVISION_CATEGORY category
report the data categories associated with a PDBX_AUDIT_REVISION_HISTORY record.
Example 1
<VRPTx:pdbx_audit_revision_categoryCategory>
<VRPTx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="1" revision_ordinal="1">
<VRPTx:category>audit_author</VRPTx:category>
</VRPTx:pdbx_audit_revision_category>
<VRPTx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="2" revision_ordinal="1">
<VRPTx:category>citation</VRPTx:category>
</VRPTx:pdbx_audit_revision_category>
<VRPTx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="3" revision_ordinal="1">
<VRPTx:category>citation_author</VRPTx:category>
</VRPTx:pdbx_audit_revision_category>
<VRPTx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="4" revision_ordinal="2">
<VRPTx:category>citation</VRPTx:category>
</VRPTx:pdbx_audit_revision_category>
</VRPTx:pdbx_audit_revision_categoryCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_audit_revision_category.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_audit_revision_detailsType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_audit_revision_details category
record descriptions of changes associated with
PDBX_AUDIT_REVISION_HISTORY records.
Example 1 -
<VRPTx:pdbx_audit_revision_detailsCategory>
<VRPTx:pdbx_audit_revision_details data_content_type="Structure model" ordinal="1" revision_ordinal="1">
<VRPTx:provider>repository</VRPTx:provider>
<VRPTx:type>Initial release</VRPTx:type>
</VRPTx:pdbx_audit_revision_details>
<VRPTx:pdbx_audit_revision_details data_content_type="Structure model" ordinal="2" revision_ordinal="7">
<VRPTx:description>Remodeling of inhibitor</VRPTx:description>
<VRPTx:provider>author</VRPTx:provider>
<VRPTx:type>Coordinate replacement</VRPTx:type>
</VRPTx:pdbx_audit_revision_details>
</VRPTx:pdbx_audit_revision_detailsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_audit_revision_details.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_audit_revision_groupType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_AUDIT_revision_group category
report the content groups associated with a PDBX_AUDIT_REVISION_HISTORY
record.
Example 1 -
<VRPTx:pdbx_audit_revision_groupCategory>
<VRPTx:pdbx_audit_revision_group data_content_type="Structure model" ordinal="1" revision_ordinal="2">
<VRPTx:group>citation</VRPTx:group>
</VRPTx:pdbx_audit_revision_group>
<VRPTx:pdbx_audit_revision_group data_content_type="Structure model" ordinal="2" revision_ordinal="3">
<VRPTx:group>sample</VRPTx:group>
</VRPTx:pdbx_audit_revision_group>
</VRPTx:pdbx_audit_revision_groupCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_audit_revision_group.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_audit_revision_historyType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_AUDIT_REVISION_HISTORY category record
the revision history for a data entry.
Example 1 -
<VRPTx:pdbx_audit_revision_historyCategory>
<VRPTx:pdbx_audit_revision_history data_content_type="Structure model" ordinal="1">
<VRPTx:major_revision>1</VRPTx:major_revision>
<VRPTx:minor_revision>0</VRPTx:minor_revision>
<VRPTx:revision_date>2017-03-01</VRPTx:revision_date>
</VRPTx:pdbx_audit_revision_history>
<VRPTx:pdbx_audit_revision_history data_content_type="Structure model" ordinal="2">
<VRPTx:major_revision>1</VRPTx:major_revision>
<VRPTx:minor_revision>1</VRPTx:minor_revision>
<VRPTx:revision_date>2017-03-08</VRPTx:revision_date>
</VRPTx:pdbx_audit_revision_history>
</VRPTx:pdbx_audit_revision_historyCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_audit_revision_history.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_audit_revision_itemType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_AUDIT_REVISION_ITEM category
report the data items associated with a PDBX_AUDIT_REVISION_HISTORY record.
Example 1
<VRPTx:pdbx_audit_revision_itemCategory>
<VRPTx:pdbx_audit_revision_item data_content_type="Structure model" ordinal="1" revision_ordinal="1">
<VRPTx:item>_atom_site.type_symbol</VRPTx:item>
</VRPTx:pdbx_audit_revision_item>
</VRPTx:pdbx_audit_revision_itemCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_audit_revision_item.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_bond_distance_limitsType |
|---|---|
| Abstract | no |
| Documentation |
This category provides a table of upper and lower distance
limits used as criteria in determining covalent bonds.
The table is organized by atom type pairs.
Example 1 - Abbreviated bond distance limit table
<VRPTx:pdbx_bond_distance_limitsCategory>
<VRPTx:pdbx_bond_distance_limits atom_type_1="N" atom_type_2="Ag">
<VRPTx:lower_limit>1.85</VRPTx:lower_limit>
<VRPTx:upper_limit>2.70</VRPTx:upper_limit>
</VRPTx:pdbx_bond_distance_limits>
<VRPTx:pdbx_bond_distance_limits atom_type_1="O" atom_type_2="Ag">
<VRPTx:lower_limit>1.85</VRPTx:lower_limit>
<VRPTx:upper_limit>2.70</VRPTx:upper_limit>
</VRPTx:pdbx_bond_distance_limits>
<VRPTx:pdbx_bond_distance_limits atom_type_1="S" atom_type_2="Ag">
<VRPTx:lower_limit>2.00</VRPTx:lower_limit>
<VRPTx:upper_limit>3.00</VRPTx:upper_limit>
</VRPTx:pdbx_bond_distance_limits>
<VRPTx:pdbx_bond_distance_limits atom_type_1="Al" atom_type_2="H">
<VRPTx:lower_limit>1.35</VRPTx:lower_limit>
<VRPTx:upper_limit>1.65</VRPTx:upper_limit>
</VRPTx:pdbx_bond_distance_limits>
<VRPTx:pdbx_bond_distance_limits atom_type_1="As" atom_type_2="H">
<VRPTx:lower_limit>1.20</VRPTx:lower_limit>
<VRPTx:upper_limit>1.60</VRPTx:upper_limit>
</VRPTx:pdbx_bond_distance_limits>
<VRPTx:pdbx_bond_distance_limits atom_type_1="N" atom_type_2="Au">
<VRPTx:lower_limit>1.80</VRPTx:lower_limit>
<VRPTx:upper_limit>2.80</VRPTx:upper_limit>
</VRPTx:pdbx_bond_distance_limits>
<VRPTx:pdbx_bond_distance_limits atom_type_1="O" atom_type_2="Au">
<VRPTx:lower_limit>1.80</VRPTx:lower_limit>
<VRPTx:upper_limit>2.80</VRPTx:upper_limit>
</VRPTx:pdbx_bond_distance_limits>
<VRPTx:pdbx_bond_distance_limits atom_type_1="S" atom_type_2="Au">
<VRPTx:lower_limit>1.80</VRPTx:lower_limit>
<VRPTx:upper_limit>3.00</VRPTx:upper_limit>
</VRPTx:pdbx_bond_distance_limits>
<VRPTx:pdbx_bond_distance_limits atom_type_1="B" atom_type_2="B">
<VRPTx:lower_limit>1.45</VRPTx:lower_limit>
<VRPTx:upper_limit>1.95</VRPTx:upper_limit>
</VRPTx:pdbx_bond_distance_limits>
<VRPTx:pdbx_bond_distance_limits atom_type_1="C" atom_type_2="B">
<VRPTx:lower_limit>1.20</VRPTx:lower_limit>
<VRPTx:upper_limit>1.85</VRPTx:upper_limit>
</VRPTx:pdbx_bond_distance_limits>
<VRPTx:pdbx_bond_distance_limits atom_type_1="F" atom_type_2="B">
<VRPTx:lower_limit>1.20</VRPTx:lower_limit>
<VRPTx:upper_limit>1.75</VRPTx:upper_limit>
</VRPTx:pdbx_bond_distance_limits>
</VRPTx:pdbx_bond_distance_limitsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_bond_distance_limits.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_branch_schemeType |
|---|---|
| Abstract | no |
| Documentation |
The PDBX_BRANCH_SCHEME category provides residue level nomenclature
mapping for branch chain entities.
Example 1 -
<VRPTx:pdbx_branch_schemeCategory>
<VRPTx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="NAG" num="1">
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_mon_id>NAG</VRPTx:auth_mon_id>
<VRPTx:auth_seq_num>1592</VRPTx:auth_seq_num>
<VRPTx:hetero>n</VRPTx:hetero>
<VRPTx:pdb_asym_id>B</VRPTx:pdb_asym_id>
<VRPTx:pdb_mon_id>NAG</VRPTx:pdb_mon_id>
<VRPTx:pdb_seq_num>1</VRPTx:pdb_seq_num>
</VRPTx:pdbx_branch_scheme>
<VRPTx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="GAL" num="2">
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_mon_id>GAL</VRPTx:auth_mon_id>
<VRPTx:auth_seq_num>1591</VRPTx:auth_seq_num>
<VRPTx:hetero>n</VRPTx:hetero>
<VRPTx:pdb_asym_id>B</VRPTx:pdb_asym_id>
<VRPTx:pdb_mon_id>GAL</VRPTx:pdb_mon_id>
<VRPTx:pdb_seq_num>2</VRPTx:pdb_seq_num>
</VRPTx:pdbx_branch_scheme>
<VRPTx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="FUC" num="3">
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_mon_id>FUC</VRPTx:auth_mon_id>
<VRPTx:auth_seq_num>1590</VRPTx:auth_seq_num>
<VRPTx:hetero>n</VRPTx:hetero>
<VRPTx:pdb_asym_id>B</VRPTx:pdb_asym_id>
<VRPTx:pdb_mon_id>FUC</VRPTx:pdb_mon_id>
<VRPTx:pdb_seq_num>3</VRPTx:pdb_seq_num>
</VRPTx:pdbx_branch_scheme>
<VRPTx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="FUC" num="4">
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_mon_id>FUC</VRPTx:auth_mon_id>
<VRPTx:auth_seq_num>1593</VRPTx:auth_seq_num>
<VRPTx:hetero>n</VRPTx:hetero>
<VRPTx:pdb_asym_id>B</VRPTx:pdb_asym_id>
<VRPTx:pdb_mon_id>FUC</VRPTx:pdb_mon_id>
<VRPTx:pdb_seq_num>4</VRPTx:pdb_seq_num>
</VRPTx:pdbx_branch_scheme>
</VRPTx:pdbx_branch_schemeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_branch_scheme.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_coordinate_modelType |
|---|---|
| Abstract | no |
| Documentation |
The details of the composition of the coordinate model.
Example 1 -
<VRPTx:pdbx_coordinate_modelCategory>
<VRPTx:pdbx_coordinate_model asym_id="A">
<VRPTx:type>CA ATOMS ONLY</VRPTx:type>
</VRPTx:pdbx_coordinate_model>
<VRPTx:pdbx_coordinate_model asym_id="B">
<VRPTx:type>CA ATOMS ONLY</VRPTx:type>
</VRPTx:pdbx_coordinate_model>
<VRPTx:pdbx_coordinate_model asym_id="X">
<VRPTx:type>P ATOMS ONLY</VRPTx:type>
</VRPTx:pdbx_coordinate_model>
<VRPTx:pdbx_coordinate_model asym_id="Y">
<VRPTx:type>P ATOMS ONLY</VRPTx:type>
</VRPTx:pdbx_coordinate_model>
</VRPTx:pdbx_coordinate_modelCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_coordinate_model.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_database_relatedType |
|---|---|
| Abstract | no |
| Documentation |
Data items in PDBX_DATABASE_RELATED contain references to entries
that are related to the this entry.
<VRPTx:pdbx_database_relatedCategory>
<VRPTx:pdbx_database_related content_type="native structure" db_id="1ABC" db_name="PDB"></VRPTx:pdbx_database_related>
</VRPTx:pdbx_database_relatedCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_database_related.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_database_statusType |
|---|---|
| Abstract | no |
| Documentation |
These are internal RCSB records to keep track of data processing
and status of the entry.
<VRPTx:pdbx_database_statusCategory>
<VRPTx:pdbx_database_status entry_id="1ABC">
<VRPTx:deposit_site>RCSB</VRPTx:deposit_site>
<VRPTx:process_site>RCSB</VRPTx:process_site>
<VRPTx:status_code>REL</VRPTx:status_code>
</VRPTx:pdbx_database_status>
</VRPTx:pdbx_database_statusCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_database_status.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_dcc_densityType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the category record various overall metrics
calculated by DCC and various wrapped programs (such as Xtriage,
pointless, REFMAC ...).
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_dcc_density.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_dcc_density_corrType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the category record calculated metrics from various
programs (such as phenix, refmac, cns, sfcheck).
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_dcc_density_corr.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_dcc_entity_geometryType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record the deviations about geometry (such as bond length, angle, dihedral, chirality, planarity) of each entity. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_dcc_geometryType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the category record the overall deviations about
geometry (such as bond length, angle, dihedral, chirality,
planarity). These data are calculated with the phenix module
model_vs_data.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_dcc_geometry.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_dcc_mapType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the category record residual map properties such as
Real Space electron density Correlation Coefficient (RSCC), real space R
factors (RSR) and the Z scores for each residue, the main/side chains.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_dcc_map.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_dcc_map_overallType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record statistics of each entry for residual map properties such as Real Space electron density Correlation Coefficient (RSCC), real space R factors (RSR) and the Z scores. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_dcc_mapmanType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the category record details from the output of mapman
used by the DCC program.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_dcc_mapman.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_dcc_mon_geometryType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record the deviations about geometry (such as bond length, angle, dihedral, chirality, planarity) of each monomer. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_dcc_rscc_mapmanType |
|---|---|
| Abstract | no |
| Documentation |
Data items in this category record residual map properties such as
correlation, real space Rfactors and the Z score calculated from
refmac and mapman.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_dcc_rscc_mapman.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_dcc_rscc_mapman_overallType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the category record overall map properties such
as correlation, real space Rfactors and the Z score calculated
from refmac and mapman.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_dcc_rscc_mapman_overall.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_diffrn_reflns_shellType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the DIFFRN_REFLNS_SHELL category record details about
the reflection data set within shells of resolution.
Example 1 - diffraction properties with shells
<VRPTx:pdbx_diffrn_reflns_shellCategory>
<VRPTx:pdbx_diffrn_reflns_shell d_res_high="5.18" d_res_low="50.00" diffrn_id="1">
<VRPTx:Rmerge_I_obs>0.029</VRPTx:Rmerge_I_obs>
<VRPTx:chi_squared>1.154</VRPTx:chi_squared>
<VRPTx:number_obs>11791</VRPTx:number_obs>
<VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs>
</VRPTx:pdbx_diffrn_reflns_shell>
<VRPTx:pdbx_diffrn_reflns_shell d_res_high="4.11" d_res_low="5.18" diffrn_id="1">
<VRPTx:Rmerge_I_obs>0.033</VRPTx:Rmerge_I_obs>
<VRPTx:chi_squared>1.098</VRPTx:chi_squared>
<VRPTx:number_obs>11717</VRPTx:number_obs>
<VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs>
</VRPTx:pdbx_diffrn_reflns_shell>
<VRPTx:pdbx_diffrn_reflns_shell d_res_high="3.59" d_res_low="4.11" diffrn_id="1">
<VRPTx:Rmerge_I_obs>0.043</VRPTx:Rmerge_I_obs>
<VRPTx:chi_squared>1.044</VRPTx:chi_squared>
<VRPTx:number_obs>11792</VRPTx:number_obs>
<VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs>
</VRPTx:pdbx_diffrn_reflns_shell>
<VRPTx:pdbx_diffrn_reflns_shell d_res_high="3.26" d_res_low="3.59" diffrn_id="1">
<VRPTx:Rmerge_I_obs>0.059</VRPTx:Rmerge_I_obs>
<VRPTx:chi_squared>1.104</VRPTx:chi_squared>
<VRPTx:number_obs>11718</VRPTx:number_obs>
<VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs>
</VRPTx:pdbx_diffrn_reflns_shell>
<VRPTx:pdbx_diffrn_reflns_shell d_res_high="3.03" d_res_low="3.26" diffrn_id="1">
<VRPTx:Rmerge_I_obs>0.087</VRPTx:Rmerge_I_obs>
<VRPTx:chi_squared>1.160</VRPTx:chi_squared>
<VRPTx:number_obs>11753</VRPTx:number_obs>
<VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs>
</VRPTx:pdbx_diffrn_reflns_shell>
<VRPTx:pdbx_diffrn_reflns_shell d_res_high="2.85" d_res_low="3.03" diffrn_id="1">
<VRPTx:Rmerge_I_obs>0.130</VRPTx:Rmerge_I_obs>
<VRPTx:chi_squared>1.169</VRPTx:chi_squared>
<VRPTx:number_obs>11811</VRPTx:number_obs>
<VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs>
</VRPTx:pdbx_diffrn_reflns_shell>
<VRPTx:pdbx_diffrn_reflns_shell d_res_high="2.71" d_res_low="2.85" diffrn_id="1">
<VRPTx:Rmerge_I_obs>0.174</VRPTx:Rmerge_I_obs>
<VRPTx:chi_squared>1.170</VRPTx:chi_squared>
<VRPTx:number_obs>11752</VRPTx:number_obs>
<VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs>
</VRPTx:pdbx_diffrn_reflns_shell>
<VRPTx:pdbx_diffrn_reflns_shell d_res_high="2.59" d_res_low="2.71" diffrn_id="1">
<VRPTx:Rmerge_I_obs>0.227</VRPTx:Rmerge_I_obs>
<VRPTx:chi_squared>1.165</VRPTx:chi_squared>
<VRPTx:number_obs>11767</VRPTx:number_obs>
<VRPTx:percent_possible_obs>100.000</VRPTx:percent_possible_obs>
</VRPTx:pdbx_diffrn_reflns_shell>
</VRPTx:pdbx_diffrn_reflns_shellCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_diffrn_reflns_shell.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_distant_solvent_atomsType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_DISTANT_SOLVENT_ATOMS category list the
solvent atoms remote from any macromolecule.
Example 1 -
<VRPTx:pdbx_distant_solvent_atomsCategory>
<VRPTx:pdbx_distant_solvent_atoms id="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>W</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>O</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>HOH</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>412</VRPTx:auth_seq_id>
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:neighbor_ligand_distance xsi:nil="true" />
<VRPTx:neighbor_macromolecule_distance>7.3</VRPTx:neighbor_macromolecule_distance>
</VRPTx:pdbx_distant_solvent_atoms>
<VRPTx:pdbx_distant_solvent_atoms id="2">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>W</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>O</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>HOH</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>413</VRPTx:auth_seq_id>
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:neighbor_ligand_distance xsi:nil="true" />
<VRPTx:neighbor_macromolecule_distance>8.4</VRPTx:neighbor_macromolecule_distance>
</VRPTx:pdbx_distant_solvent_atoms>
<VRPTx:pdbx_distant_solvent_atoms id="3">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>W</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>O</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>HOH</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>414</VRPTx:auth_seq_id>
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:neighbor_ligand_distance xsi:nil="true" />
<VRPTx:neighbor_macromolecule_distance>7.2</VRPTx:neighbor_macromolecule_distance>
</VRPTx:pdbx_distant_solvent_atoms>
<VRPTx:pdbx_distant_solvent_atoms id="4">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>W</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>O</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>HOH</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>415</VRPTx:auth_seq_id>
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:neighbor_ligand_distance xsi:nil="true" />
<VRPTx:neighbor_macromolecule_distance>8.3</VRPTx:neighbor_macromolecule_distance>
</VRPTx:pdbx_distant_solvent_atoms>
</VRPTx:pdbx_distant_solvent_atomsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_distant_solvent_atoms.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_domainType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_DOMAIN category record information
about domain definitions.
A domain need not correspond to a completely polypeptide chain;
it can be composed of one or more segments in a single chain,
or by segments from more than one chain.
Example 1 -
<VRPTx:pdbx_domainCategory>
<VRPTx:pdbx_domain id="d1">
<VRPTx:details>Chains A, B</VRPTx:details>
</VRPTx:pdbx_domain>
<VRPTx:pdbx_domain id="d2">
<VRPTx:details>Asym_id D Residues 1-134</VRPTx:details>
</VRPTx:pdbx_domain>
</VRPTx:pdbx_domainCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_domain.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_domain_rangeType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_DOMAIN_RANGE category identify the
beginning and ending points of polypeptide chain segments
that form all or part of a domain.
Example 1 -
<VRPTx:pdbx_domain_rangeCategory>
<VRPTx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="A" beg_label_comp_id="PRO" beg_label_seq_id="1" domain_id="d1" end_label_alt_id="A" end_label_asym_id="A" end_label_comp_id="GLY" end_label_seq_id="29"></VRPTx:pdbx_domain_range>
<VRPTx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="B" beg_label_comp_id="PRO" beg_label_seq_id="31" domain_id="d1" end_label_alt_id="A" end_label_asym_id="B" end_label_comp_id="GLY" end_label_seq_id="59"></VRPTx:pdbx_domain_range>
<VRPTx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="C" beg_label_comp_id="PRO" beg_label_seq_id="61" domain_id="d1" end_label_alt_id="A" end_label_asym_id="B" end_label_comp_id="GLY" end_label_seq_id="89"></VRPTx:pdbx_domain_range>
<VRPTx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="D" beg_label_comp_id="PRO" beg_label_seq_id="91" domain_id="d2" end_label_alt_id="A" end_label_asym_id="D" end_label_comp_id="GLY" end_label_seq_id="119"></VRPTx:pdbx_domain_range>
<VRPTx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="E" beg_label_comp_id="PRO" beg_label_seq_id="121" domain_id="d2" end_label_alt_id="A" end_label_asym_id="E" end_label_comp_id="GLY" end_label_seq_id="149"></VRPTx:pdbx_domain_range>
<VRPTx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="F" beg_label_comp_id="PRO" beg_label_seq_id="151" domain_id="d2" end_label_alt_id="A" end_label_asym_id="F" end_label_comp_id="GLY" end_label_seq_id="179"></VRPTx:pdbx_domain_range>
</VRPTx:pdbx_domain_rangeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_domain_range.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_atom_inclusionType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record fraction of atoms that are inside the surface at a given contour level. Ref: User guide to the wwPDB EM validation reports 9. Map-model fit 9.2 Atom inclusion Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_atom_inclusionCategory> <VRPTx:pdbx_em_atom_inclusion id="1"> <VRPTx:atom_inclusion_title>Fraction of model inside the map</VRPTx:atom_inclusion_title> <VRPTx:atom_type>all non-hydrogen atoms</VRPTx:atom_type> <VRPTx:contour_level_title>Contour level</VRPTx:contour_level_title> </VRPTx:pdbx_em_atom_inclusion> <VRPTx:pdbx_em_atom_inclusion id="2"> <VRPTx:atom_inclusion_title>Fraction of model inside the map</VRPTx:atom_inclusion_title> <VRPTx:atom_type>backbone atoms</VRPTx:atom_type> <VRPTx:contour_level_title>Contour level</VRPTx:contour_level_title> </VRPTx:pdbx_em_atom_inclusion> </VRPTx:pdbx_em_atom_inclusionCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_atom_inclusion_markerType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record atom inclusion plot. Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_atom_inclusion_markerCategory> <VRPTx:pdbx_em_atom_inclusion_marker ordinal="1" plot_id="1"> <VRPTx:atom_inclusion>1</VRPTx:atom_inclusion> <VRPTx:contour_level>-0.097199</VRPTx:contour_level> </VRPTx:pdbx_em_atom_inclusion_marker> <VRPTx:pdbx_em_atom_inclusion_marker ordinal="2" plot_id="1"> <VRPTx:atom_inclusion>1</VRPTx:atom_inclusion> <VRPTx:contour_level>-0.095008</VRPTx:contour_level> </VRPTx:pdbx_em_atom_inclusion_marker> <VRPTx:pdbx_em_atom_inclusion_marker ordinal="3" plot_id="1"> <VRPTx:atom_inclusion>1</VRPTx:atom_inclusion> <VRPTx:contour_level>-0.092817</VRPTx:contour_level> </VRPTx:pdbx_em_atom_inclusion_marker> <VRPTx:pdbx_em_atom_inclusion_marker ordinal="4" plot_id="1"> <VRPTx:atom_inclusion>1</VRPTx:atom_inclusion> <VRPTx:contour_level>-0.090626</VRPTx:contour_level> </VRPTx:pdbx_em_atom_inclusion_marker> <VRPTx:pdbx_em_atom_inclusion_marker ordinal="5" plot_id="1"> <VRPTx:atom_inclusion>1</VRPTx:atom_inclusion> <VRPTx:contour_level>-0.088435</VRPTx:contour_level> </VRPTx:pdbx_em_atom_inclusion_marker> </VRPTx:pdbx_em_atom_inclusion_markerCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_density_distributionType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record map-value distribution of the primary EM volume. Ref: User guide to the wwPDB EM validation reports 7. Map analysis 7.1 Map value distribution Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_density_distributionCategory> <VRPTx:pdbx_em_density_distribution id="1"> <VRPTx:map_value_title>Map-value</VRPTx:map_value_title> <VRPTx:voxel_count_scale>log10</VRPTx:voxel_count_scale> <VRPTx:voxel_count_title>Number of voxels</VRPTx:voxel_count_title> </VRPTx:pdbx_em_density_distribution> </VRPTx:pdbx_em_density_distributionCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_density_distribution_markerType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record map-value distribution plot of the primary EM volume. Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_density_distribution_markerCategory> <VRPTx:pdbx_em_density_distribution_marker ordinal="1" plot_id="1"> <VRPTx:map_value>-0.0971993208</VRPTx:map_value> <VRPTx:voxel_count>1.6812412374</VRPTx:voxel_count> </VRPTx:pdbx_em_density_distribution_marker> <VRPTx:pdbx_em_density_distribution_marker ordinal="2" plot_id="1"> <VRPTx:map_value>-0.0949910375</VRPTx:map_value> <VRPTx:voxel_count>0</VRPTx:voxel_count> </VRPTx:pdbx_em_density_distribution_marker> <VRPTx:pdbx_em_density_distribution_marker ordinal="3" plot_id="1"> <VRPTx:map_value>-0.0927827541</VRPTx:map_value> <VRPTx:voxel_count>1.3802112417</VRPTx:voxel_count> </VRPTx:pdbx_em_density_distribution_marker> <VRPTx:pdbx_em_density_distribution_marker ordinal="4" plot_id="1"> <VRPTx:map_value>-0.0905744708</VRPTx:map_value> <VRPTx:voxel_count>0</VRPTx:voxel_count> </VRPTx:pdbx_em_density_distribution_marker> <VRPTx:pdbx_em_density_distribution_marker ordinal="5" plot_id="1"> <VRPTx:map_value>-0.0883661875</VRPTx:map_value> <VRPTx:voxel_count>1.8573324964</VRPTx:voxel_count> </VRPTx:pdbx_em_density_distribution_marker> </VRPTx:pdbx_em_density_distribution_markerCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_fsc_curveType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record Fourier-Shell Correlation (FSC) curve. Ref: User guide to the wwPDB EM validation reports 8. FSC validation 8.1 Calculated FSC 8.2 Author provided FSC Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_fsc_curveCategory> <VRPTx:pdbx_em_fsc_curve id="1"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc</VRPTx:title> </VRPTx:pdbx_em_fsc_curve> <VRPTx:pdbx_em_fsc_curve id="2"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc</VRPTx:title> </VRPTx:pdbx_em_fsc_curve> </VRPTx:pdbx_em_fsc_curveCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_fsc_curve_markerType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record row data to plot Fourier-Shell Correlation (FSC) curve. Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_fsc_curve_markerCategory> <VRPTx:pdbx_em_fsc_curve_marker ordinal="1" plot_id="1"> <VRPTx:correlation_coef>1</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_curve_marker> <VRPTx:pdbx_em_fsc_curve_marker ordinal="2" plot_id="1"> <VRPTx:correlation_coef>0.9999</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0046</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_curve_marker> <VRPTx:pdbx_em_fsc_curve_marker ordinal="3" plot_id="1"> <VRPTx:correlation_coef>1</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0091</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_curve_marker> <VRPTx:pdbx_em_fsc_curve_marker ordinal="4" plot_id="1"> <VRPTx:correlation_coef>1</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0137</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_curve_marker> <VRPTx:pdbx_em_fsc_curve_marker ordinal="5" plot_id="1"> <VRPTx:correlation_coef>0.9999</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0182</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_curve_marker> </VRPTx:pdbx_em_fsc_curve_markerCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_fsc_cutoff_curveType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record Fourier-Shell Correlation (FSC) cut-off curve that represents a given criterion. Ref: User guide to the wwPDB EM validation reports 8. FSC validation 8.1 Calculated FSC 8.2 Author provided FSC Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_fsc_cutoff_curveCategory> <VRPTx:pdbx_em_fsc_cutoff_curve id="1"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc_one-bit</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="2"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc_0.143</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="3"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc_0.5</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="4"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc_0.333</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="5"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc_half-bit</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="6"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>calculated_fsc_3sigma</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="7"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc_3sigma</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="8"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc_one-bit</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="9"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc_0.143</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="10"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc_0.5</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="11"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc_0.333</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> <VRPTx:pdbx_em_fsc_cutoff_curve id="12"> <VRPTx:correlation_coef_title>Correlation coefficient</VRPTx:correlation_coef_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> <VRPTx:title>author_provided_fsc_half-bit</VRPTx:title> </VRPTx:pdbx_em_fsc_cutoff_curve> </VRPTx:pdbx_em_fsc_cutoff_curveCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_fsc_cutoff_curve_markerType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record row data to plot Fourier-Shell Correlation (FSC) cut-off curve that represents a given criterion. Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_fsc_cutoff_curve_markerCategory> <VRPTx:pdbx_em_fsc_cutoff_curve_marker ordinal="1" plot_id="1"> <VRPTx:correlation_coef>1</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_cutoff_curve_marker> <VRPTx:pdbx_em_fsc_cutoff_curve_marker ordinal="2" plot_id="1"> <VRPTx:correlation_coef>0.607</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0046</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_cutoff_curve_marker> <VRPTx:pdbx_em_fsc_cutoff_curve_marker ordinal="3" plot_id="1"> <VRPTx:correlation_coef>0.5135</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0091</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_cutoff_curve_marker> <VRPTx:pdbx_em_fsc_cutoff_curve_marker ordinal="4" plot_id="1"> <VRPTx:correlation_coef>0.4674</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0137</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_cutoff_curve_marker> <VRPTx:pdbx_em_fsc_cutoff_curve_marker ordinal="5" plot_id="1"> <VRPTx:correlation_coef>0.4401</VRPTx:correlation_coef> <VRPTx:spatial_frequency>0.0182</VRPTx:spatial_frequency> </VRPTx:pdbx_em_fsc_cutoff_curve_marker> </VRPTx:pdbx_em_fsc_cutoff_curve_markerCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_fsc_resolutionType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record estimated global resolutions from Fourier-Shell Correlation (FSC) curve using various criteria for single-particle and subtomogram averaging methods. Ref: User guide to the wwPDB EM validation reports 8. FSC validation 8.1 Resolution estimate Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_fsc_resolutionCategory> <VRPTx:pdbx_em_fsc_resolution criterion="one-bit" source="calculated_fsc"> <VRPTx:correlation_coef>0.3396</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>1</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>1</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.69</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.3715</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="0.143" source="calculated_fsc"> <VRPTx:correlation_coef>0.143</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>1</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>2</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.38</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4195</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="0.5" source="calculated_fsc"> <VRPTx:correlation_coef>0.5</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>1</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>3</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.79</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.3587</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="0.333" source="calculated_fsc"> <VRPTx:correlation_coef>0.333</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>1</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>4</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.65</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.3768</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="half-bit" source="calculated_fsc"> <VRPTx:correlation_coef>0.178</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>1</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>5</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.48</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4039</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="3sigma" source="calculated_fsc"> <VRPTx:correlation_coef>0.0116</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>1</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>6</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.16</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4636</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="3sigma" source="author_provided_fsc"> <VRPTx:correlation_coef>0.0108</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>2</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>7</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.01</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.498</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="one-bit" source="author_provided_fsc"> <VRPTx:correlation_coef>0.3387</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>2</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>8</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.32</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4304</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="0.143" source="author_provided_fsc"> <VRPTx:correlation_coef>0.143</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>2</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>9</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.15</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4648</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="0.5" source="author_provided_fsc"> <VRPTx:correlation_coef>0.5</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>2</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>10</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.48</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4027</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="0.333" source="author_provided_fsc"> <VRPTx:correlation_coef>0.333</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>2</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>11</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.32</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.431</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> <VRPTx:pdbx_em_fsc_resolution criterion="half-bit" source="author_provided_fsc"> <VRPTx:correlation_coef>0.1772</VRPTx:correlation_coef> <VRPTx:fsc_curve_id>2</VRPTx:fsc_curve_id> <VRPTx:fsc_cutoff_curve_id>12</VRPTx:fsc_cutoff_curve_id> <VRPTx:resolution>2.16</VRPTx:resolution> <VRPTx:resolution_unit>A</VRPTx:resolution_unit> <VRPTx:spatial_frequency>0.4625</VRPTx:spatial_frequency> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_fsc_resolution> </VRPTx:pdbx_em_fsc_resolutionCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_rapsType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record Rotationally Averaged Power Spectrum (RAPS) for the primary EM volume (map). The RAPS provides insight into the data processing steps leading to the map, in terms of: CTF correction, Temperature factor correction, Low and/or high-pass filtering, Masking artifacts. The RAPS is only generated for cubic volumes. Ref: User guide to the wwPDB EM validation reports 7. Map analysis 7.3 Rotationally averaged power spectrum Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_rapsCategory> <VRPTx:pdbx_em_raps id="1"> <VRPTx:power_scale>log10</VRPTx:power_scale> <VRPTx:power_title>Intensity</VRPTx:power_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_raps> </VRPTx:pdbx_em_rapsCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_raps_markerType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record Rotationally Averaged Power Spectrum (RAPS) plot for the primary EM volume (map). Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_raps_markerCategory> <VRPTx:pdbx_em_raps_marker ordinal="1" plot_id="1"> <VRPTx:power>5.0361312138</VRPTx:power> <VRPTx:spatial_frequency>0</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raps_marker> <VRPTx:pdbx_em_raps_marker ordinal="2" plot_id="1"> <VRPTx:power>4.6874764273</VRPTx:power> <VRPTx:spatial_frequency>0.0045551653</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raps_marker> <VRPTx:pdbx_em_raps_marker ordinal="3" plot_id="1"> <VRPTx:power>4.0158584907</VRPTx:power> <VRPTx:spatial_frequency>0.0091103306</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raps_marker> <VRPTx:pdbx_em_raps_marker ordinal="4" plot_id="1"> <VRPTx:power>3.3080813094</VRPTx:power> <VRPTx:spatial_frequency>0.0136654959</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raps_marker> <VRPTx:pdbx_em_raps_marker ordinal="5" plot_id="1"> <VRPTx:power>3.3633413357</VRPTx:power> <VRPTx:spatial_frequency>0.0182206612</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raps_marker> </VRPTx:pdbx_em_raps_markerCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_raw_rapsType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record Rotationally Averaged Power Spectrum (RAPS) for raw EM volume (map). The RAPS provides insight into the data processing steps leading to the map, in terms of: CTF correction, Temperature factor correction, Low and/or high-pass filtering, Masking artifacts. The RAPS is only generated for cubic volumes. Ref: User guide to the wwPDB EM validation reports 7. Map analysis 7.3 Rotationally averaged power spectrum Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_raw_rapsCategory> <VRPTx:pdbx_em_raw_raps id="1"> <VRPTx:power_scale>log10</VRPTx:power_scale> <VRPTx:power_title>Intensity</VRPTx:power_title> <VRPTx:spatial_frequency_title>Spatial frequency</VRPTx:spatial_frequency_title> <VRPTx:spatial_frequency_unit>1/A</VRPTx:spatial_frequency_unit> </VRPTx:pdbx_em_raw_raps> </VRPTx:pdbx_em_raw_rapsCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_raw_raps_markerType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record Rotationally Averaged Power Spectrum (RAPS) plot for raw EM volume (map). Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_raw_raps_markerCategory> <VRPTx:pdbx_em_raw_raps_marker ordinal="1" plot_id="1"> <VRPTx:power>5.0361312138</VRPTx:power> <VRPTx:spatial_frequency>0</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raw_raps_marker> <VRPTx:pdbx_em_raw_raps_marker ordinal="2" plot_id="1"> <VRPTx:power>4.6874764273</VRPTx:power> <VRPTx:spatial_frequency>0.0045551653</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raw_raps_marker> <VRPTx:pdbx_em_raw_raps_marker ordinal="3" plot_id="1"> <VRPTx:power>4.0158584907</VRPTx:power> <VRPTx:spatial_frequency>0.0091103306</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raw_raps_marker> <VRPTx:pdbx_em_raw_raps_marker ordinal="4" plot_id="1"> <VRPTx:power>3.3080813094</VRPTx:power> <VRPTx:spatial_frequency>0.0136654959</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raw_raps_marker> <VRPTx:pdbx_em_raw_raps_marker ordinal="5" plot_id="1"> <VRPTx:power>3.3633413357</VRPTx:power> <VRPTx:spatial_frequency>0.0182206612</VRPTx:spatial_frequency> </VRPTx:pdbx_em_raw_raps_marker> </VRPTx:pdbx_em_raw_raps_markerCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_validate_map_modelType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record EM map-model validation for each residue Ref: User guide to the wwPDB EM validation reports 9. Map-Model fit 9.3 Atom inclusion by residue |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_validate_map_model_entityType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record EM map-model validation for each entity Ref: User guide to the wwPDB EM validation reports 9. Map-Model fit 9.2 Atom inclusion |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_validate_map_model_overallType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record overall EM map-model validation of each entry. Ref: User guide to the wwPDB EM validation reports 7. Map analysis 7.2 Volume estimate by contour -> recommended_contour_level 9. Map-Model fit 9.2 Q-score mapped to coordinate model -> Q-score 9.4 Atom inclusion -> atom_inclusion_main, atom_inclusion_all |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_volume_estimateType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record volume estimation of the primary EM volume. Ref: User guide to the wwPDB EM validation reports 7. Map analysis 7.2 Volume estimate by contour Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_volume_estimateCategory> <VRPTx:pdbx_em_volume_estimate id="1"> <VRPTx:contour_level_title>Contour level</VRPTx:contour_level_title> <VRPTx:enclosed_volume_title>Volume</VRPTx:enclosed_volume_title> <VRPTx:enclosed_volume_unit>nm3</VRPTx:enclosed_volume_unit> </VRPTx:pdbx_em_volume_estimate> </VRPTx:pdbx_em_volume_estimateCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_em_volume_estimate_markerType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record volume estimation plot of the primary EM volume. Example 1 - based on PDB entry 6RJH. <VRPTx:pdbx_em_volume_estimate_markerCategory> <VRPTx:pdbx_em_volume_estimate_marker ordinal="1" plot_id="1"> <VRPTx:contour_level>-0.0971993208</VRPTx:contour_level> <VRPTx:enclosed_volume>10768.9715137</VRPTx:enclosed_volume> </VRPTx:pdbx_em_volume_estimate_marker> <VRPTx:pdbx_em_volume_estimate_marker ordinal="2" plot_id="1"> <VRPTx:contour_level>-0.0950082897</VRPTx:contour_level> <VRPTx:enclosed_volume>10768.9583621</VRPTx:enclosed_volume> </VRPTx:pdbx_em_volume_estimate_marker> <VRPTx:pdbx_em_volume_estimate_marker ordinal="3" plot_id="1"> <VRPTx:contour_level>-0.0928172586</VRPTx:contour_level> <VRPTx:enclosed_volume>10768.9583621</VRPTx:enclosed_volume> </VRPTx:pdbx_em_volume_estimate_marker> <VRPTx:pdbx_em_volume_estimate_marker ordinal="4" plot_id="1"> <VRPTx:contour_level>-0.0906262274</VRPTx:contour_level> <VRPTx:enclosed_volume>10768.9517863</VRPTx:enclosed_volume> </VRPTx:pdbx_em_volume_estimate_marker> <VRPTx:pdbx_em_volume_estimate_marker ordinal="5" plot_id="1"> <VRPTx:contour_level>-0.0884351963</VRPTx:contour_level> <VRPTx:enclosed_volume>10768.9517863</VRPTx:enclosed_volume> </VRPTx:pdbx_em_volume_estimate_marker> </VRPTx:pdbx_em_volume_estimate_markerCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_entity_assemblyType |
|---|---|
| Abstract | no |
| Documentation |
The PDBX_ENTITY_ASSEMBLY category provides a chemical description
of the biological assembly studied in terms of its constituent
entities.
A complex composed of one copy of entities 1 and 2.
<VRPTx:pdbx_entity_assemblyCategory>
<VRPTx:pdbx_entity_assembly entity_id="1" id="1">
<VRPTx:biol_id>1</VRPTx:biol_id>
<VRPTx:num_copies>1</VRPTx:num_copies>
</VRPTx:pdbx_entity_assembly>
<VRPTx:pdbx_entity_assembly entity_id="2" id="1">
<VRPTx:biol_id>1</VRPTx:biol_id>
<VRPTx:num_copies>1</VRPTx:num_copies>
</VRPTx:pdbx_entity_assembly>
</VRPTx:pdbx_entity_assemblyCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_entity_assembly.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_entity_branchType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_ENTITY_BRANCH category specify the list
of branched entities and the type.
Example 1 -
<VRPTx:pdbx_entity_branchCategory>
<VRPTx:pdbx_entity_branch entity_id="2">
<VRPTx:type>oligosaccharide</VRPTx:type>
</VRPTx:pdbx_entity_branch>
</VRPTx:pdbx_entity_branchCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_entity_branch.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_entity_branch_descriptorType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_ENTITY_BRANCH_DESCRIPTOR category provide
string descriptors of entity chemical structure.
Example 1 -
<VRPTx:pdbx_entity_branch_descriptorCategory>
<VRPTx:pdbx_entity_branch_descriptor ordinal="1">
<VRPTx:descriptor>[][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}</VRPTx:descriptor>
<VRPTx:entity_id>1</VRPTx:entity_id>
<VRPTx:program>PDB-CARE</VRPTx:program>
<VRPTx:program_version>Beta</VRPTx:program_version>
<VRPTx:type>LINUCS</VRPTx:type>
</VRPTx:pdbx_entity_branch_descriptor>
</VRPTx:pdbx_entity_branch_descriptorCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_entity_branch_descriptor.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_entity_branch_linkType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_ENTITY_BRANCH_LINK category give details about
the linkages between components within a branched entity.
Example 1 - base on PDB entry 2WMG
<VRPTx:pdbx_entity_branch_linkCategory>
<VRPTx:pdbx_entity_branch_link link_id="1">
<VRPTx:atom_id_1>O4</VRPTx:atom_id_1>
<VRPTx:atom_id_2>C1</VRPTx:atom_id_2>
<VRPTx:atom_stereo_config_2>R</VRPTx:atom_stereo_config_2>
<VRPTx:comp_id_1>NAG</VRPTx:comp_id_1>
<VRPTx:comp_id_2>GAL</VRPTx:comp_id_2>
<VRPTx:entity_branch_list_num_1>1</VRPTx:entity_branch_list_num_1>
<VRPTx:entity_branch_list_num_2>2</VRPTx:entity_branch_list_num_2>
<VRPTx:entity_id>2</VRPTx:entity_id>
<VRPTx:leaving_atom_id_1>HO4</VRPTx:leaving_atom_id_1>
<VRPTx:leaving_atom_id_2>O1</VRPTx:leaving_atom_id_2>
<VRPTx:value_order>sing</VRPTx:value_order>
</VRPTx:pdbx_entity_branch_link>
<VRPTx:pdbx_entity_branch_link link_id="2">
<VRPTx:atom_id_1>O2</VRPTx:atom_id_1>
<VRPTx:atom_id_2>C1</VRPTx:atom_id_2>
<VRPTx:atom_stereo_config_2>R</VRPTx:atom_stereo_config_2>
<VRPTx:comp_id_1>GAL</VRPTx:comp_id_1>
<VRPTx:comp_id_2>FUC</VRPTx:comp_id_2>
<VRPTx:entity_branch_list_num_1>2</VRPTx:entity_branch_list_num_1>
<VRPTx:entity_branch_list_num_2>3</VRPTx:entity_branch_list_num_2>
<VRPTx:entity_id>2</VRPTx:entity_id>
<VRPTx:leaving_atom_id_1>HO2</VRPTx:leaving_atom_id_1>
<VRPTx:leaving_atom_id_2>O1</VRPTx:leaving_atom_id_2>
<VRPTx:value_order>sing</VRPTx:value_order>
</VRPTx:pdbx_entity_branch_link>
<VRPTx:pdbx_entity_branch_link link_id="3">
<VRPTx:atom_id_1>O3</VRPTx:atom_id_1>
<VRPTx:atom_id_2>C1</VRPTx:atom_id_2>
<VRPTx:atom_stereo_config_2>R</VRPTx:atom_stereo_config_2>
<VRPTx:comp_id_1>NAG</VRPTx:comp_id_1>
<VRPTx:comp_id_2>FUC</VRPTx:comp_id_2>
<VRPTx:entity_branch_list_num_1>1</VRPTx:entity_branch_list_num_1>
<VRPTx:entity_branch_list_num_2>4</VRPTx:entity_branch_list_num_2>
<VRPTx:entity_id>2</VRPTx:entity_id>
<VRPTx:leaving_atom_id_1>HO3</VRPTx:leaving_atom_id_1>
<VRPTx:leaving_atom_id_2>O1</VRPTx:leaving_atom_id_2>
<VRPTx:value_order>sing</VRPTx:value_order>
</VRPTx:pdbx_entity_branch_link>
</VRPTx:pdbx_entity_branch_linkCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_entity_branch_link.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_entity_branch_listType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_ENTITY_BRANCH_LIST category specify the list
of monomers in a branched entity. Allowance is made for the possibility
of microheterogeneity in a sample by allowing a given sequence
number to be correlated with more than one monomer ID. The
corresponding ATOM_SITE entries should reflect this
heterogeneity.
Example 1 -
<VRPTx:pdbx_entity_branch_listCategory>
<VRPTx:pdbx_entity_branch_list comp_id="NAG" entity_id="2" num="1">
<VRPTx:hetero>n</VRPTx:hetero>
</VRPTx:pdbx_entity_branch_list>
<VRPTx:pdbx_entity_branch_list comp_id="GAL" entity_id="2" num="2">
<VRPTx:hetero>n</VRPTx:hetero>
</VRPTx:pdbx_entity_branch_list>
<VRPTx:pdbx_entity_branch_list comp_id="FUC" entity_id="2" num="3">
<VRPTx:hetero>n</VRPTx:hetero>
</VRPTx:pdbx_entity_branch_list>
<VRPTx:pdbx_entity_branch_list comp_id="FUC" entity_id="2" num="4">
<VRPTx:hetero>n</VRPTx:hetero>
</VRPTx:pdbx_entity_branch_list>
</VRPTx:pdbx_entity_branch_listCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_entity_branch_list.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_entity_descriptorType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_ENTITY_DESCRIPTOR category provide string descriptors of entity chemical structure. Example 1 - <VRPTx:pdbx_entity_descriptorCategory> <VRPTx:pdbx_entity_descriptor ordinal="1"> <VRPTx:descriptor>[][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}</VRPTx:descriptor> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:program>PDB-CARE</VRPTx:program> <VRPTx:program_version>Beta</VRPTx:program_version> <VRPTx:type>LINUCS</VRPTx:type> </VRPTx:pdbx_entity_descriptor> </VRPTx:pdbx_entity_descriptorCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_entity_nonpolyType |
|---|---|
| Abstract | no |
| Documentation |
The PDBX_ENTITY_NONPOLY category provides a mapping between
entity and the nonpolymer component
Example 1 - based on PDB entry 3LTQ
<VRPTx:pdbx_entity_nonpolyCategory>
<VRPTx:pdbx_entity_nonpoly entity_id="2">
<VRPTx:comp_id>TB</VRPTx:comp_id>
<VRPTx:name>TERBIUM(III) ION</VRPTx:name>
</VRPTx:pdbx_entity_nonpoly>
<VRPTx:pdbx_entity_nonpoly entity_id="3">
<VRPTx:comp_id>ACT</VRPTx:comp_id>
<VRPTx:name>ACETATE ION</VRPTx:name>
</VRPTx:pdbx_entity_nonpoly>
<VRPTx:pdbx_entity_nonpoly entity_id="4">
<VRPTx:comp_id>SO4</VRPTx:comp_id>
<VRPTx:name>SULFATE ION</VRPTx:name>
</VRPTx:pdbx_entity_nonpoly>
<VRPTx:pdbx_entity_nonpoly entity_id="5">
<VRPTx:comp_id>HOH</VRPTx:comp_id>
<VRPTx:name>water</VRPTx:name>
</VRPTx:pdbx_entity_nonpoly>
</VRPTx:pdbx_entity_nonpolyCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_entity_nonpoly.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_entity_poly_comp_link_listType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_ENTITY_POLY_COMP_LINK_LIST category enumerate
the linkages between components within the polymer entity.
Example 1 -
<VRPTx:pdbx_entity_poly_comp_link_listCategory>
<VRPTx:pdbx_entity_poly_comp_link_list link_id="1">
<VRPTx:atom_id_1 xsi:nil="true" />
<VRPTx:atom_id_2 xsi:nil="true" />
<VRPTx:atom_stereo_config_1 xsi:nil="true" />
<VRPTx:atom_stereo_config_2 xsi:nil="true" />
<VRPTx:comp_id_1 xsi:nil="true" />
<VRPTx:comp_id_2 xsi:nil="true" />
<VRPTx:entity_comp_num_1>1</VRPTx:entity_comp_num_1>
<VRPTx:entity_comp_num_2>2</VRPTx:entity_comp_num_2>
<VRPTx:entity_id>1</VRPTx:entity_id>
<VRPTx:leaving_atom_id_1 xsi:nil="true" />
<VRPTx:leaving_atom_id_2 xsi:nil="true" />
<VRPTx:value_order>sing</VRPTx:value_order>
</VRPTx:pdbx_entity_poly_comp_link_list>
</VRPTx:pdbx_entity_poly_comp_link_listCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_entity_poly_comp_link_list.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_entry_detailsType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_ENTRY_DETAILS category provide additional
details about this entry.
Example 1 -
<VRPTx:pdbx_entry_detailsCategory>
<VRPTx:pdbx_entry_details entry_id="1ABC">
<VRPTx:nonpolymer_details>Inhibitor VX4A in this entry adopts a highly strained conformation
about C32 inorder to fit into the cleft about the active site.</VRPTx:nonpolymer_details>
</VRPTx:pdbx_entry_details>
</VRPTx:pdbx_entry_detailsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_entry_details.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_helical_symmetryType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_HELICAL_SYMMETRY category record details about the
helical symmetry group associated with this entry.
Example 1 -
<VRPTx:pdbx_helical_symmetryCategory>
<VRPTx:pdbx_helical_symmetry entry_id="1ABC">
<VRPTx:circular_symmetry>1</VRPTx:circular_symmetry>
<VRPTx:dyad_axis>no</VRPTx:dyad_axis>
<VRPTx:n_subunits_divisor>1</VRPTx:n_subunits_divisor>
<VRPTx:number_of_operations>35</VRPTx:number_of_operations>
<VRPTx:rise_per_n_subunits>6.10</VRPTx:rise_per_n_subunits>
<VRPTx:rotation_per_n_subunits>131.84</VRPTx:rotation_per_n_subunits>
</VRPTx:pdbx_helical_symmetry>
</VRPTx:pdbx_helical_symmetryCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_helical_symmetry.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_missing_nmr_star_itemType |
|---|---|
| Abstract | no |
| Documentation | Items in the PDBX_MISSING_NMR_STAR_ITEM category provide information about required NMR-STAR V3 data items to parse assigned chemical shifts. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_assigned_chem_shift_listType |
|---|---|
| Abstract | no |
| Documentation |
Items in the PDBX_NMR_ASSIGNED_CHEM_SHIFT_LIST category provide information about a list of reported assigned chemical shift values.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_assigned_chem_shift_list.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_chem_shift_annotationType |
|---|---|
| Abstract | no |
| Documentation | Items in the PDBX_NMR_CHEM_SHIFT_ANNOTATION category provide information about various derived values from assigned chemical shifts. e.g. random coil index. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_chem_shift_completenessType |
|---|---|
| Abstract | no |
| Documentation | Items in the PDBX_NMR_CHEM_SHIFT_COMPLETENESS category provide information about completeness of assigned chemical shifts. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_chem_shift_re_offsetType |
|---|---|
| Abstract | no |
| Documentation | Items in the PDBX_NMR_CHEM_SHIFT_RE_OFFSET category provide information about chemical shift reference correction based on assigned chemical shifts. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_constraintsType |
|---|---|
| Abstract | no |
| Documentation |
This section provides a tabulation of constraint data.
This example uses the data from the MCP-1 structure determination. Remember
this is a dimer so there are intersubunit constraints as well as intrasubunit
constraints.
<VRPTx:pdbx_nmr_constraintsCategory>
<VRPTx:pdbx_nmr_constraints entry_id="1ABC">
<VRPTx:NOE_constraints_total>4458</VRPTx:NOE_constraints_total>
<VRPTx:NOE_intraresidue_total_count>1144</VRPTx:NOE_intraresidue_total_count>
<VRPTx:NOE_long_range_total_count>1356</VRPTx:NOE_long_range_total_count>
<VRPTx:NOE_medium_range_total_count>1004</VRPTx:NOE_medium_range_total_count>
<VRPTx:NOE_sequential_total_count>272</VRPTx:NOE_sequential_total_count>
<VRPTx:protein_phi_angle_constraints_total_count>96</VRPTx:protein_phi_angle_constraints_total_count>
</VRPTx:pdbx_nmr_constraints>
</VRPTx:pdbx_nmr_constraintsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_constraints.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_detailsType |
|---|---|
| Abstract | no |
| Documentation |
Experimental details of the NMR study that have not been
described elsewhere in this deposition.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_details.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_dihedral_angle_violationType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record all dihedral angle restraint violations of the ensemble. Ref: User guide to the wwPDB NMR validation reports 10. Dihedral-angle violation analysis 10.5 All violated dihedral-angle restraints |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_dihedral_angle_violation_ensembleType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record violations of dihedral angle restraints for each virtual ensemble alternating the size of an ensemble. Ref: User guide to the wwPDB NMR validation reports 10. Dihedral-angle violation analysis 10.3 Dihedral-angle violation statistics for the ensemble |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_dihedral_angle_violation_modelType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record violations of dihedral angle restraints for each model. Ref: User guide to the wwPDB NMR validation reports 10. Dihedral-angle violation analysis 10.2 Dihedral-angle violation statistics for each model |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_dihedral_angle_violation_pluralType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record potentially severe violations of dihedral angle restraints, which occurred in multiple coordinate models of the ensemble. Ref: User guide to the wwPDB NMR validation reports 10. Dihedral-angle violation analysis 10.4 Most violated dihedral angle restraints in the ensemble |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_dihedral_angle_violation_summaryType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record violations of dihedral angle restraints. Ref: User guide to the wwPDB NMR validation reports 10. Dihedral-angle violation analysis 10.1 Summary of dihedral-angle violations |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_distance_violationType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record all distance restraint violations of the ensemble. Ref: User guide to the wwPDB NMR validation reports 9. Distance violation analysis 9.5 All violated distance restraints |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_distance_violation_ensembleType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record violations of distance restraints for each virtual ensemble alternating the size of an ensemble. Ref: User guide to the wwPDB NMR validation reports 9. Distance violation analysis 9.3 Distance violation statistics for the ensemble |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_distance_violation_modelType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record violations of distance restraints for each model. Ref: User guide to the wwPDB NMR validation reports 9. Distance violation analysis 9.2 Distance violation statistics for each model |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_distance_violation_pluralType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record potentially severe violations of distance restraints, which occurred in multiple coordinate models of the ensemble. Ref: User guide to the wwPDB NMR validation reports 9. Distance violation analysis 9.4 Most violated distance restraints in the ensemble |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_distance_violation_summaryType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record violations of distance restraints. Ref: User guide to the wwPDB NMR validation reports 9. Distance violation analysis 9.1 Summary of distance violations |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_ensembleType |
|---|---|
| Abstract | no |
| Documentation |
This category contains the information that describes the
ensemble of deposited structures. If only an average structure
has been deposited skip this section.
This example uses the data from the MCP-1 study.
<VRPTx:pdbx_nmr_ensembleCategory>
<VRPTx:pdbx_nmr_ensemble entry_id="1ABC">
<VRPTx:conformer_selection_criteria>structures with the least restraint violations</VRPTx:conformer_selection_criteria>
<VRPTx:conformers_calculated_total_number>40</VRPTx:conformers_calculated_total_number>
<VRPTx:conformers_submitted_total_number>20</VRPTx:conformers_submitted_total_number>
<VRPTx:representative_conformer>1</VRPTx:representative_conformer>
</VRPTx:pdbx_nmr_ensemble>
</VRPTx:pdbx_nmr_ensembleCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_ensemble.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_ensemble_rmsType |
|---|---|
| Abstract | no |
| Documentation |
Structural statistics are derived from molecular dynamics and simulated annealing
programs.
This example is derived from the MCP-1 structure calculation statistics.
For this structure the statistics were calculated over residues 5-69 for
both the monomer and dimer .
<VRPTx:pdbx_nmr_ensemble_rmsCategory>
<VRPTx:pdbx_nmr_ensemble_rms entry_id="1ABC">
<VRPTx:atom_type>all heavy atoms</VRPTx:atom_type>
<VRPTx:chain_range_begin>A</VRPTx:chain_range_begin>
<VRPTx:chain_range_end>A</VRPTx:chain_range_end>
<VRPTx:distance_rms_dev>0.22</VRPTx:distance_rms_dev>
<VRPTx:distance_rms_dev_error>0.06</VRPTx:distance_rms_dev_error>
<VRPTx:residue_range_begin>5</VRPTx:residue_range_begin>
<VRPTx:residue_range_end>69</VRPTx:residue_range_end>
</VRPTx:pdbx_nmr_ensemble_rms>
</VRPTx:pdbx_nmr_ensemble_rmsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_ensemble_rms.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_exptlType |
|---|---|
| Abstract | no |
| Documentation |
In this section, enter information on those experiments that were
used to generate constraint data. For each NMR experiment indicate
which sample and which sample conditions were used for the experiment.
This example was taken from the MCP-1 study.
<VRPTx:pdbx_nmr_exptlCategory>
<VRPTx:pdbx_nmr_exptl conditions_id="1" experiment_id="1" solution_id="3">
<VRPTx:type>3D_15N-separated_NOESY</VRPTx:type>
</VRPTx:pdbx_nmr_exptl>
<VRPTx:pdbx_nmr_exptl conditions_id="1" experiment_id="2" solution_id="1">
<VRPTx:type>3D_13C-separated_NOESY</VRPTx:type>
</VRPTx:pdbx_nmr_exptl>
<VRPTx:pdbx_nmr_exptl conditions_id="2" experiment_id="3" solution_id="1">
<VRPTx:type>4D_13C/15N-separated_NOESY</VRPTx:type>
</VRPTx:pdbx_nmr_exptl>
<VRPTx:pdbx_nmr_exptl conditions_id="1" experiment_id="4" solution_id="1">
<VRPTx:type>4D_13C-separated_NOESY</VRPTx:type>
</VRPTx:pdbx_nmr_exptl>
<VRPTx:pdbx_nmr_exptl conditions_id="1" experiment_id="5" solution_id="1">
<VRPTx:type>3D_15N-separated_ROESY</VRPTx:type>
</VRPTx:pdbx_nmr_exptl>
<VRPTx:pdbx_nmr_exptl conditions_id="1" experiment_id="6" solution_id="3">
<VRPTx:type>3D_13C-separated_ROESY</VRPTx:type>
</VRPTx:pdbx_nmr_exptl>
</VRPTx:pdbx_nmr_exptlCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_exptl.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_exptl_sampleType |
|---|---|
| Abstract | no |
| Documentation |
The chemical constituents of
each NMR sample. Each sample is identified by a number and
each component in the sample is identified by name.
Example 1 -
This example was taken from the study of MCP-1 which is a dimer under the
conditions studied. Three solutions with different isotope compositions were
studied.
<VRPTx:pdbx_nmr_exptl_sampleCategory>
<VRPTx:pdbx_nmr_exptl_sample component="MCP-1" solution_id="1">
<VRPTx:concentration>2</VRPTx:concentration>
<VRPTx:concentration_units>mM</VRPTx:concentration_units>
<VRPTx:isotopic_labeling>U-15N,13C</VRPTx:isotopic_labeling>
</VRPTx:pdbx_nmr_exptl_sample>
<VRPTx:pdbx_nmr_exptl_sample component="H2O" solution_id="1">
<VRPTx:concentration>90</VRPTx:concentration>
<VRPTx:concentration_units>%</VRPTx:concentration_units>
<VRPTx:isotopic_labeling xsi:nil="true" />
</VRPTx:pdbx_nmr_exptl_sample>
<VRPTx:pdbx_nmr_exptl_sample component="D2O" solution_id="1">
<VRPTx:concentration>10</VRPTx:concentration>
<VRPTx:concentration_units>%</VRPTx:concentration_units>
<VRPTx:isotopic_labeling xsi:nil="true" />
</VRPTx:pdbx_nmr_exptl_sample>
</VRPTx:pdbx_nmr_exptl_sampleCategory>
Example 2 -
This example was taken from the study of MCP-1 which is a dimer under the
conditions studied. Three solutions with different isotope compositions were
studied.
<VRPTx:pdbx_nmr_exptl_sampleCategory>
<VRPTx:pdbx_nmr_exptl_sample component="MCP-1" solution_id="2">
<VRPTx:concentration>1</VRPTx:concentration>
<VRPTx:concentration_units>mM</VRPTx:concentration_units>
<VRPTx:isotopic_labeling>U-50% 15N</VRPTx:isotopic_labeling>
</VRPTx:pdbx_nmr_exptl_sample>
<VRPTx:pdbx_nmr_exptl_sample component="H2O" solution_id="2">
<VRPTx:concentration>90</VRPTx:concentration>
<VRPTx:concentration_units>%</VRPTx:concentration_units>
<VRPTx:isotopic_labeling xsi:nil="true" />
</VRPTx:pdbx_nmr_exptl_sample>
<VRPTx:pdbx_nmr_exptl_sample component="D2O" solution_id="2">
<VRPTx:concentration>10</VRPTx:concentration>
<VRPTx:concentration_units>%</VRPTx:concentration_units>
<VRPTx:isotopic_labeling xsi:nil="true" />
</VRPTx:pdbx_nmr_exptl_sample>
</VRPTx:pdbx_nmr_exptl_sampleCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_exptl_sample.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_exptl_sample_conditionsType |
|---|---|
| Abstract | no |
| Documentation |
The experimental conditions used to for each sample. Each set of conditions
is identified by a numerical code.
This example was taken from a pH stability study.
<VRPTx:pdbx_nmr_exptl_sample_conditionsCategory>
<VRPTx:pdbx_nmr_exptl_sample_conditions conditions_id="1">
<VRPTx:ionic_strength>25mM NaCl</VRPTx:ionic_strength>
<VRPTx:pH>7</VRPTx:pH>
<VRPTx:pressure>ambient</VRPTx:pressure>
<VRPTx:temperature>298</VRPTx:temperature>
</VRPTx:pdbx_nmr_exptl_sample_conditions>
<VRPTx:pdbx_nmr_exptl_sample_conditions conditions_id="2">
<VRPTx:ionic_strength>25mM NaCl</VRPTx:ionic_strength>
<VRPTx:pH>3</VRPTx:pH>
<VRPTx:pressure>ambient</VRPTx:pressure>
<VRPTx:temperature>298</VRPTx:temperature>
</VRPTx:pdbx_nmr_exptl_sample_conditions>
</VRPTx:pdbx_nmr_exptl_sample_conditionsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_exptl_sample_conditions.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_force_constantsType |
|---|---|
| Abstract | no |
| Documentation |
The final force constants, including units, employed for the various
experimental constraints, covalent geometry constraints, and the non-bonded
interaction terms in the target function used for simulated annealing.
This example is taken from a study of BAF, a dimeric DNA binding protein.
The final force constants in the target function used for simulated
annealing are: Experimental Constraint terms: Distance (NOE,H-bonds),
Torsion angles, J coupling, 13C shifts, 1H shifts, Dipolar coupling,
D isotope shifts Covalent Geometry Constraint terms: Bond lengths,
Angles, Impropers Non-bonded Interaction terms: van der Waals,
Type of van der Waals term, Conformational database potential,
Radius of gyration.
<VRPTx:pdbx_nmr_force_constantsCategory>
<VRPTx:pdbx_nmr_force_constants entry_id="1ABC">
<VRPTx:covalent_geom_bond_term>1000.</VRPTx:covalent_geom_bond_term>
<VRPTx:covalent_geom_bond_term_units>kcal/mol/A**2</VRPTx:covalent_geom_bond_term_units>
<VRPTx:exptl_13C_shift_term>0.5</VRPTx:exptl_13C_shift_term>
<VRPTx:exptl_13C_shift_term_units>kcal/mol/ppm**2</VRPTx:exptl_13C_shift_term_units>
<VRPTx:exptl_1H_shift_term>7.5</VRPTx:exptl_1H_shift_term>
<VRPTx:exptl_1H_shift_term_units>kcal/mol/ppm**2</VRPTx:exptl_1H_shift_term_units>
<VRPTx:exptl_J_coupling_term>1.</VRPTx:exptl_J_coupling_term>
<VRPTx:exptl_J_coupling_term_units>kcal/mol/Hz**2</VRPTx:exptl_J_coupling_term_units>
<VRPTx:exptl_distance_term>30.</VRPTx:exptl_distance_term>
<VRPTx:exptl_distance_term_units>kcal/mol/A**2</VRPTx:exptl_distance_term_units>
<VRPTx:exptl_torsion_angles_term>200.</VRPTx:exptl_torsion_angles_term>
<VRPTx:exptl_torsion_angles_term_units>kcal/mol/rad**2</VRPTx:exptl_torsion_angles_term_units>
<VRPTx:non-bonded_inter_van_der_Waals_term_type>4.</VRPTx:non-bonded_inter_van_der_Waals_term_type>
<VRPTx:non-bonded_inter_van_der_Waals_term_units>kcal/mol/A**4</VRPTx:non-bonded_inter_van_der_Waals_term_units>
</VRPTx:pdbx_nmr_force_constants>
</VRPTx:pdbx_nmr_force_constantsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_force_constants.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_refineType |
|---|---|
| Abstract | no |
| Documentation |
Describe the method and details of the refinement of the deposited structure.
This example is drawn from the MCP-1 structure.
<VRPTx:pdbx_nmr_refineCategory>
<VRPTx:pdbx_nmr_refine entry_id="1ABC" software_ordinal="1">
<VRPTx:method>torsion angle dynamics</VRPTx:method>
</VRPTx:pdbx_nmr_refine>
</VRPTx:pdbx_nmr_refineCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_refine.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_representativeType |
|---|---|
| Abstract | no |
| Documentation |
An average structure is often calculated in addition to the ensemble, or one
of the ensemble is selected as a representative structure. This section
describes selection of the representative structure.
This example is drawn from the MCP-1 structure.
<VRPTx:pdbx_nmr_representativeCategory>
<VRPTx:pdbx_nmr_representative entry_id="1ABC">
<VRPTx:conformer_id>15</VRPTx:conformer_id>
<VRPTx:selection_criteria>lowest energy</VRPTx:selection_criteria>
</VRPTx:pdbx_nmr_representative>
</VRPTx:pdbx_nmr_representativeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_representative.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_restraint_listType |
|---|---|
| Abstract | no |
| Documentation | Items in the PDBX_NMR_RESTRAINT_LIST category provide information about a list of NMR restraints. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_restraint_summaryType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record NMR restraints analysis. Ref: User guide to the wwPDB NMR validation reports 8. NMR restraints analysis 8.1 Conformationally restricting restraints |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_restraint_violationType |
|---|---|
| Abstract | no |
| Documentation | Data items in the category record residual violations of conformationally restricting restraints in different bins based on its magnitude of violation. Ref: User guide to the wwPDB NMR validation reports 8. NMR restraints analysis 8.2 Residual restraint violations |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_softwareType |
|---|---|
| Abstract | no |
| Documentation |
Description of the software that was used for data collection, data processing,
data analysis, structure calculations and refinement. The description should
include the name of the software, the author of the software and the version used.
This example describes the software used in the MCP-1 study.
<VRPTx:pdbx_nmr_softwareCategory>
<VRPTx:pdbx_nmr_software ordinal="1">
<VRPTx:authors>Bruker</VRPTx:authors>
<VRPTx:classification>collection</VRPTx:classification>
<VRPTx:name>UXNMR</VRPTx:name>
<VRPTx:version>940501.3</VRPTx:version>
</VRPTx:pdbx_nmr_software>
<VRPTx:pdbx_nmr_software ordinal="2">
<VRPTx:authors>Hare</VRPTx:authors>
<VRPTx:classification>processing</VRPTx:classification>
<VRPTx:name>FELIX</VRPTx:name>
<VRPTx:version>1.1</VRPTx:version>
</VRPTx:pdbx_nmr_software>
<VRPTx:pdbx_nmr_software ordinal="3">
<VRPTx:authors>Kraulis</VRPTx:authors>
<VRPTx:classification>data analysis</VRPTx:classification>
<VRPTx:name>ANSIG</VRPTx:name>
<VRPTx:version>3.0</VRPTx:version>
</VRPTx:pdbx_nmr_software>
<VRPTx:pdbx_nmr_software ordinal="4">
<VRPTx:authors>Brunger</VRPTx:authors>
<VRPTx:classification>structure calculation</VRPTx:classification>
<VRPTx:name>X-PLOR</VRPTx:name>
<VRPTx:version>3.8</VRPTx:version>
</VRPTx:pdbx_nmr_software>
</VRPTx:pdbx_nmr_softwareCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_software.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_spectrometerType |
|---|---|
| Abstract | no |
| Documentation |
The details about each spectrometer used to collect data for this
deposition.
The instruments described here are the ones used for the MCP-1 studies.
<VRPTx:pdbx_nmr_spectrometerCategory>
<VRPTx:pdbx_nmr_spectrometer spectrometer_id="1">
<VRPTx:field_strength>600</VRPTx:field_strength>
<VRPTx:type>Bruker AMX</VRPTx:type>
</VRPTx:pdbx_nmr_spectrometer>
<VRPTx:pdbx_nmr_spectrometer spectrometer_id="2">
<VRPTx:field_strength>500</VRPTx:field_strength>
<VRPTx:type>Bruker AMX</VRPTx:type>
</VRPTx:pdbx_nmr_spectrometer>
</VRPTx:pdbx_nmr_spectrometerCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nmr_spectrometer.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_unmapped_chem_shiftType |
|---|---|
| Abstract | no |
| Documentation | Items in the PDBX_NMR_UNMAPPED_CHEM_SHIFT category provide information about assigned chemical shifts not mapped to atoms in the NMR structure. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nmr_unparsed_chem_shiftType |
|---|---|
| Abstract | no |
| Documentation | Items in the PDBX_NMR_UNPARSED_CHEM_SHIFT category provide information about assigned chemical shifts not parsed. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_nonpoly_schemeType |
|---|---|
| Abstract | no |
| Documentation |
The PDBX_NONPOLY_SCHEME category provides residue level nomenclature
mapping for non-polymer entities.
Example 1 -
<VRPTx:pdbx_nonpoly_schemeCategory>
<VRPTx:pdbx_nonpoly_scheme asym_id="C" ndb_seq_num="100">
<VRPTx:auth_mon_id>HOH</VRPTx:auth_mon_id>
<VRPTx:auth_seq_num>100</VRPTx:auth_seq_num>
<VRPTx:entity_id>3</VRPTx:entity_id>
<VRPTx:mon_id>HOH</VRPTx:mon_id>
<VRPTx:pdb_ins_code xsi:nil="true" />
<VRPTx:pdb_mon_id>HOH</VRPTx:pdb_mon_id>
<VRPTx:pdb_seq_num>100</VRPTx:pdb_seq_num>
<VRPTx:pdb_strand_id>C</VRPTx:pdb_strand_id>
</VRPTx:pdbx_nonpoly_scheme>
</VRPTx:pdbx_nonpoly_schemeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_nonpoly_scheme.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_percentile_conditionsType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_PERCENTILE_CONDITIONS category describe conditions to calculate percentile rank representations of each validation metric in the wwPDB validation report. For example, relative evaluation for X-ray structure is obtained by by comparing other X-ray structures having similar resolution. If there are no conditions by default, absolute evaluation is calculated based on all available PDB structures determined by the same methodology. Example 1 - <VRPTx:pdbx_percentile_conditionsCategory> <VRPTx:pdbx_percentile_conditions id="1"> <VRPTx:ls_d_res_high xsi:nil="true" /> <VRPTx:ls_d_res_low xsi:nil="true" /> <VRPTx:number_entries_total>101464</VRPTx:number_entries_total> </VRPTx:pdbx_percentile_conditions> <VRPTx:pdbx_percentile_conditions id="2"> <VRPTx:ls_d_res_high>1.9</VRPTx:ls_d_res_high> <VRPTx:ls_d_res_low>1.9</VRPTx:ls_d_res_low> <VRPTx:number_entries_total>5100</VRPTx:number_entries_total> </VRPTx:pdbx_percentile_conditions> </VRPTx:pdbx_percentile_conditionsCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_percentile_entity_viewType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_PERCENTILE_ENTITY_VIEW category describe a percentile rank representation of defined validation metric for each entity in the wwPDB validation report. Example 1 - <VRPTx:pdbx_percentile_entity_viewCategory> <VRPTx:pdbx_percentile_entity_view conditions_id="1" label_asym_id="A" type="RSRZ_outliers_percent"> <VRPTx:conditions_label>absolute</VRPTx:conditions_label> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:rank>100.0</VRPTx:rank> </VRPTx:pdbx_percentile_entity_view> <VRPTx:pdbx_percentile_entity_view conditions_id="2" label_asym_id="A" type="RSRZ_outliers_percent"> <VRPTx:conditions_label>relative</VRPTx:conditions_label> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:rank>100.0</VRPTx:rank> </VRPTx:pdbx_percentile_entity_view> <VRPTx:pdbx_percentile_entity_view conditions_id="1" label_asym_id="B" type="RSRZ_outliers_percent"> <VRPTx:conditions_label>absolute</VRPTx:conditions_label> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:rank>100.0</VRPTx:rank> </VRPTx:pdbx_percentile_entity_view> <VRPTx:pdbx_percentile_entity_view conditions_id="2" label_asym_id="B" type="RSRZ_outliers_percent"> <VRPTx:conditions_label>relative</VRPTx:conditions_label> <VRPTx:entity_id>1</VRPTx:entity_id> <VRPTx:rank>100.0</VRPTx:rank> </VRPTx:pdbx_percentile_entity_view> </VRPTx:pdbx_percentile_entity_viewCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_percentile_listType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_PERCENTILE_LIST category describe a set of percentile rank representations of each validation metric in the wwPDB validation report. Example 1 - <VRPTx:pdbx_percentile_listCategory> <VRPTx:pdbx_percentile_list entry_id="5U9B"> <VRPTx:name>all,1.8,xray</VRPTx:name> </VRPTx:pdbx_percentile_list> </VRPTx:pdbx_percentile_listCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_percentile_viewType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_PERCENTILE_VIEW category describe a percentile rank representation of defined validation metric in the wwPDB validation report. Example 1 - <VRPTx:pdbx_percentile_viewCategory> <VRPTx:pdbx_percentile_view conditions_id="1" entry_id="5B1L" type="'all_atom_clashscore"> <VRPTx:conditions_label>absolute</VRPTx:conditions_label> <VRPTx:rank>66.9</VRPTx:rank> </VRPTx:pdbx_percentile_view> <VRPTx:pdbx_percentile_view conditions_id="1" entry_id="5B1L" type="'RSRZ_outliers_percent"> <VRPTx:conditions_label>absolute</VRPTx:conditions_label> <VRPTx:rank>100.0</VRPTx:rank> </VRPTx:pdbx_percentile_view> <VRPTx:pdbx_percentile_view conditions_id="2" entry_id="5B1L" type="'all_atom_clashscore"> <VRPTx:conditions_label>relative</VRPTx:conditions_label> <VRPTx:rank>62.5</VRPTx:rank> </VRPTx:pdbx_percentile_view> <VRPTx:pdbx_percentile_view conditions_id="2" entry_id="5B1L" type="'RSRZ_outliers_percent"> <VRPTx:conditions_label>relative</VRPTx:conditions_label> <VRPTx:rank>100.0</VRPTx:rank> </VRPTx:pdbx_percentile_view> </VRPTx:pdbx_percentile_viewCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_phasing_MAD_setType |
|---|---|
| Abstract | no |
| Documentation |
Record details about each phasing set: (Note: the phasing
set is different from data set. for example: if there are
three data sets, the inflection point (IP), the peak (PK)
and the high remote (HR), the combination of the phasing
set will be IP_iso, PK_iso (the isomorphous repleacement
with HR as 'native'), IP_ano, PK_ano and HR_ano (the
anomalous difference with itself). Therefore, there are
five set used for phasing.
Example 1 - three wavelengths
<VRPTx:pdbx_phasing_MAD_setCategory>
<VRPTx:pdbx_phasing_MAD_set id="ISO_1">
<VRPTx:R_cullis_acentric>0.000</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric>
<VRPTx:d_res_high>2.00</VRPTx:d_res_high>
<VRPTx:d_res_low>22.60</VRPTx:d_res_low>
<VRPTx:reflns_acentric>5387</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>471</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set>
<VRPTx:pdbx_phasing_MAD_set id="ISO_2">
<VRPTx:R_cullis_acentric>0.803</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.718</VRPTx:R_cullis_centric>
<VRPTx:d_res_high>2.00</VRPTx:d_res_high>
<VRPTx:d_res_low>22.60</VRPTx:d_res_low>
<VRPTx:reflns_acentric>5365</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>469</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set>
<VRPTx:pdbx_phasing_MAD_set id="ISO_3">
<VRPTx:R_cullis_acentric>0.658</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.500</VRPTx:R_cullis_centric>
<VRPTx:d_res_high>2.00</VRPTx:d_res_high>
<VRPTx:d_res_low>22.60</VRPTx:d_res_low>
<VRPTx:reflns_acentric>5317</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>460</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set>
<VRPTx:pdbx_phasing_MAD_set id="ANO_1">
<VRPTx:R_cullis_acentric>0.841</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric>
<VRPTx:d_res_high>2.00</VRPTx:d_res_high>
<VRPTx:d_res_low>22.60</VRPTx:d_res_low>
<VRPTx:reflns_acentric>5278</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>0</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set>
<VRPTx:pdbx_phasing_MAD_set id="ANO_2">
<VRPTx:R_cullis_acentric>0.649</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric>
<VRPTx:d_res_high>2.00</VRPTx:d_res_high>
<VRPTx:d_res_low>22.60</VRPTx:d_res_low>
<VRPTx:reflns_acentric>5083</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>0</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set>
<VRPTx:pdbx_phasing_MAD_set id="ANO_3">
<VRPTx:R_cullis_acentric>0.829</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric>
<VRPTx:d_res_high>2.00</VRPTx:d_res_high>
<VRPTx:d_res_low>22.60</VRPTx:d_res_low>
<VRPTx:reflns_acentric>5329</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>0</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set>
</VRPTx:pdbx_phasing_MAD_setCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_phasing_MAD_set.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_phasing_MAD_set_shellType |
|---|---|
| Abstract | no |
| Documentation |
The same as category pdbx_phasing_MAD_set, but
broken into shells.
Example 1 - three wavelengths (SHARP example)
<VRPTx:pdbx_phasing_MAD_set_shellCategory>
<VRPTx:pdbx_phasing_MAD_set_shell d_res_high="7.77" d_res_low="22.60" id="ISO_1">
<VRPTx:R_cullis_acentric>0.000</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric>
<VRPTx:power_acentric>0.000</VRPTx:power_acentric>
<VRPTx:power_centric>0.000</VRPTx:power_centric>
<VRPTx:reflns_acentric>64</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>23</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set_shell>
<VRPTx:pdbx_phasing_MAD_set_shell d_res_high="5.67" d_res_low="7.77" id="ISO_1">
<VRPTx:R_cullis_acentric>0.000</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric>
<VRPTx:power_acentric>0.000</VRPTx:power_acentric>
<VRPTx:power_centric>0.000</VRPTx:power_centric>
<VRPTx:reflns_acentric>130</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>32</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set_shell>
<VRPTx:pdbx_phasing_MAD_set_shell d_res_high="4.68" d_res_low="5.67" id="ISO_1">
<VRPTx:R_cullis_acentric>0.000</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric>
<VRPTx:power_acentric>0.000</VRPTx:power_acentric>
<VRPTx:power_centric>0.000</VRPTx:power_centric>
<VRPTx:reflns_acentric>182</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>27</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set_shell>
<VRPTx:pdbx_phasing_MAD_set_shell d_res_high="4.07" d_res_low="4.68" id="ISO_1">
<VRPTx:R_cullis_acentric>0.000</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric>
<VRPTx:power_acentric>0.000</VRPTx:power_acentric>
<VRPTx:power_centric>0.000</VRPTx:power_centric>
<VRPTx:reflns_acentric>207</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>24</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set_shell>
<VRPTx:pdbx_phasing_MAD_set_shell d_res_high="7.77" d_res_low="22.60" id="ANO_1">
<VRPTx:R_cullis_acentric>0.610</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric>
<VRPTx:power_acentric>1.804</VRPTx:power_acentric>
<VRPTx:power_centric>0.000</VRPTx:power_centric>
<VRPTx:reflns_acentric>62</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>0</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set_shell>
<VRPTx:pdbx_phasing_MAD_set_shell d_res_high="5.67" d_res_low="7.77" id="ANO_1">
<VRPTx:R_cullis_acentric>0.532</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric>
<VRPTx:power_acentric>2.382</VRPTx:power_acentric>
<VRPTx:power_centric>0.000</VRPTx:power_centric>
<VRPTx:reflns_acentric>129</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>0</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set_shell>
<VRPTx:pdbx_phasing_MAD_set_shell d_res_high="4.68" d_res_low="5.67" id="ANO_1">
<VRPTx:R_cullis_acentric>0.673</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric>
<VRPTx:power_acentric>1.858</VRPTx:power_acentric>
<VRPTx:power_centric>0.000</VRPTx:power_centric>
<VRPTx:reflns_acentric>178</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>0</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set_shell>
<VRPTx:pdbx_phasing_MAD_set_shell d_res_high="4.07" d_res_low="4.68" id="ANO_1">
<VRPTx:R_cullis_acentric>0.755</VRPTx:R_cullis_acentric>
<VRPTx:R_cullis_centric>0.000</VRPTx:R_cullis_centric>
<VRPTx:power_acentric>1.605</VRPTx:power_acentric>
<VRPTx:power_centric>0.000</VRPTx:power_centric>
<VRPTx:reflns_acentric>204</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>0</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_set_shell>
</VRPTx:pdbx_phasing_MAD_set_shellCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_phasing_MAD_set_shell.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_phasing_MAD_set_siteType |
|---|---|
| Abstract | no |
| Documentation |
Record the details (coordinates etc.) of anomalous scatters.
Example 1 - anomalous scatters is Se
<VRPTx:pdbx_phasing_MAD_set_siteCategory>
<VRPTx:pdbx_phasing_MAD_set_site id="1">
<VRPTx:Cartn_x>25.9407</VRPTx:Cartn_x>
<VRPTx:Cartn_y>-0.103471</VRPTx:Cartn_y>
<VRPTx:Cartn_z>17.4094</VRPTx:Cartn_z>
<VRPTx:atom_type_symbol>SE</VRPTx:atom_type_symbol>
<VRPTx:b_iso>15.2561</VRPTx:b_iso>
<VRPTx:occupancy>1</VRPTx:occupancy>
</VRPTx:pdbx_phasing_MAD_set_site>
<VRPTx:pdbx_phasing_MAD_set_site id="2">
<VRPTx:Cartn_x>30.6534</VRPTx:Cartn_x>
<VRPTx:Cartn_y>6.62359</VRPTx:Cartn_y>
<VRPTx:Cartn_z>9.93063</VRPTx:Cartn_z>
<VRPTx:atom_type_symbol>SE</VRPTx:atom_type_symbol>
<VRPTx:b_iso>12.9102</VRPTx:b_iso>
<VRPTx:occupancy>1</VRPTx:occupancy>
</VRPTx:pdbx_phasing_MAD_set_site>
<VRPTx:pdbx_phasing_MAD_set_site id="3">
<VRPTx:Cartn_x>-3.26506</VRPTx:Cartn_x>
<VRPTx:Cartn_y>15.5546</VRPTx:Cartn_y>
<VRPTx:Cartn_z>53.9529</VRPTx:Cartn_z>
<VRPTx:atom_type_symbol>SE</VRPTx:atom_type_symbol>
<VRPTx:b_iso>30.5239</VRPTx:b_iso>
<VRPTx:occupancy>1</VRPTx:occupancy>
</VRPTx:pdbx_phasing_MAD_set_site>
</VRPTx:pdbx_phasing_MAD_set_siteCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_phasing_MAD_set_site.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_phasing_MAD_shellType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_PHASING_MAD_SHELL category record details about
the phasing of the structure, when methods involving multiple
anomalous dispersion techniques are involved (note: the
values are overall, but broken down into shells of resolution)
Example 1 -
<VRPTx:pdbx_phasing_MAD_shellCategory>
<VRPTx:pdbx_phasing_MAD_shell d_res_high="7.77" d_res_low="22.60">
<VRPTx:fom_acentric>0.886</VRPTx:fom_acentric>
<VRPTx:fom_centric>0.641</VRPTx:fom_centric>
<VRPTx:reflns_acentric>64</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>23</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_shell>
<VRPTx:pdbx_phasing_MAD_shell d_res_high="5.67" d_res_low="7.77">
<VRPTx:fom_acentric>0.863</VRPTx:fom_acentric>
<VRPTx:fom_centric>0.642</VRPTx:fom_centric>
<VRPTx:reflns_acentric>132</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>32</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_shell>
<VRPTx:pdbx_phasing_MAD_shell d_res_high="4.68" d_res_low="5.67">
<VRPTx:fom_acentric>0.842</VRPTx:fom_acentric>
<VRPTx:fom_centric>0.737</VRPTx:fom_centric>
<VRPTx:reflns_acentric>182</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>27</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_shell>
<VRPTx:pdbx_phasing_MAD_shell d_res_high="4.07" d_res_low="4.68">
<VRPTx:fom_acentric>0.789</VRPTx:fom_acentric>
<VRPTx:fom_centric>0.682</VRPTx:fom_centric>
<VRPTx:reflns_acentric>209</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>24</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_shell>
<VRPTx:pdbx_phasing_MAD_shell d_res_high="3.65" d_res_low="4.07">
<VRPTx:fom_acentric>0.772</VRPTx:fom_acentric>
<VRPTx:fom_centric>0.633</VRPTx:fom_centric>
<VRPTx:reflns_acentric>246</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>27</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_shell>
<VRPTx:pdbx_phasing_MAD_shell d_res_high="3.34" d_res_low="3.65">
<VRPTx:fom_acentric>0.752</VRPTx:fom_acentric>
<VRPTx:fom_centric>0.700</VRPTx:fom_centric>
<VRPTx:reflns_acentric>260</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>31</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_MAD_shell>
</VRPTx:pdbx_phasing_MAD_shellCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_phasing_MAD_shell.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_phasing_MRType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_PHASING_MR category record details about
molecular replacement.
Example 1 - molecular replacement example from program CNS.
<VRPTx:pdbx_phasing_MRCategory>
<VRPTx:pdbx_phasing_MR entry_id="ABC001">
<VRPTx:correlation_coeff_Fo_to_Fc>0.586</VRPTx:correlation_coeff_Fo_to_Fc>
<VRPTx:d_res_high_rotation>3.8</VRPTx:d_res_high_rotation>
<VRPTx:d_res_high_translation>4.0</VRPTx:d_res_high_translation>
<VRPTx:d_res_low_rotation>13.0</VRPTx:d_res_low_rotation>
<VRPTx:d_res_low_translation>15.0</VRPTx:d_res_low_translation>
<VRPTx:method_rotation>real-space rotation search</VRPTx:method_rotation>
<VRPTx:method_translation>gerneral using PC-refinement= e2e2</VRPTx:method_translation>
<VRPTx:packing>0.3086</VRPTx:packing>
<VRPTx:reflns_percent_rotation>97.8</VRPTx:reflns_percent_rotation>
<VRPTx:reflns_percent_translation>97.7</VRPTx:reflns_percent_translation>
<VRPTx:sigma_F_rotation>1.0</VRPTx:sigma_F_rotation>
<VRPTx:sigma_F_translation>0</VRPTx:sigma_F_translation>
</VRPTx:pdbx_phasing_MR>
</VRPTx:pdbx_phasing_MRCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_phasing_MR.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_phasing_dmType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_PHASING_DM category record details about
density modification
Example 1 - density modification from resolve
<VRPTx:pdbx_phasing_dmCategory>
<VRPTx:pdbx_phasing_dm entry_id="ABC001">
<VRPTx:fom>0.85</VRPTx:fom>
<VRPTx:fom_acentric>0.85</VRPTx:fom_acentric>
<VRPTx:fom_centric>0.79</VRPTx:fom_centric>
<VRPTx:reflns>12486</VRPTx:reflns>
<VRPTx:reflns_acentric>11351</VRPTx:reflns_acentric>
<VRPTx:reflns_centric>1135</VRPTx:reflns_centric>
</VRPTx:pdbx_phasing_dm>
</VRPTx:pdbx_phasing_dmCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_phasing_dm.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_phasing_dm_shellType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_PHASING_DM_SHELL category record details about
density modification in resolution shell.
Example 1 - density modification with shells
<VRPTx:pdbx_phasing_dm_shellCategory>
<VRPTx:pdbx_phasing_dm_shell d_res_high="7.73" d_res_low="100.00">
<VRPTx:delta_phi_final>24.7</VRPTx:delta_phi_final>
<VRPTx:fom>0.879</VRPTx:fom>
<VRPTx:reflns>502</VRPTx:reflns>
</VRPTx:pdbx_phasing_dm_shell>
<VRPTx:pdbx_phasing_dm_shell d_res_high="6.24" d_res_low="7.73">
<VRPTx:delta_phi_final>29.2</VRPTx:delta_phi_final>
<VRPTx:fom>0.857</VRPTx:fom>
<VRPTx:reflns>506</VRPTx:reflns>
</VRPTx:pdbx_phasing_dm_shell>
<VRPTx:pdbx_phasing_dm_shell d_res_high="5.50" d_res_low="6.24">
<VRPTx:delta_phi_final>29.2</VRPTx:delta_phi_final>
<VRPTx:fom>0.838</VRPTx:fom>
<VRPTx:reflns>504</VRPTx:reflns>
</VRPTx:pdbx_phasing_dm_shell>
<VRPTx:pdbx_phasing_dm_shell d_res_high="5.02" d_res_low="5.50">
<VRPTx:delta_phi_final>25.3</VRPTx:delta_phi_final>
<VRPTx:fom>0.851</VRPTx:fom>
<VRPTx:reflns>502</VRPTx:reflns>
</VRPTx:pdbx_phasing_dm_shell>
<VRPTx:pdbx_phasing_dm_shell d_res_high="4.67" d_res_low="5.02">
<VRPTx:delta_phi_final>22.7</VRPTx:delta_phi_final>
<VRPTx:fom>0.831</VRPTx:fom>
<VRPTx:reflns>503</VRPTx:reflns>
</VRPTx:pdbx_phasing_dm_shell>
</VRPTx:pdbx_phasing_dm_shellCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_phasing_dm_shell.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_point_symmetryType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_POINT_SYMMETRY category record details about the
point symmetry group associated with this entry.
Example 1 -
<VRPTx:pdbx_point_symmetryCategory>
<VRPTx:pdbx_point_symmetry entry_id="1ABC">
<VRPTx:H-M_notation>532</VRPTx:H-M_notation>
<VRPTx:Schoenflies_symbol>I</VRPTx:Schoenflies_symbol>
</VRPTx:pdbx_point_symmetry>
</VRPTx:pdbx_point_symmetryCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_point_symmetry.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_poly_seq_schemeType |
|---|---|
| Abstract | no |
| Documentation |
The PDBX_POLY_SEQ_SCHEME category provides residue level nomenclature
mapping for polymer entities.
Example 1 - based on NDB entry DDFB25
<VRPTx:pdbx_poly_seq_schemeCategory>
<VRPTx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DC" seq_id="1">
<VRPTx:auth_mon_id>DC</VRPTx:auth_mon_id>
<VRPTx:auth_seq_num>1</VRPTx:auth_seq_num>
<VRPTx:ndb_seq_num>1</VRPTx:ndb_seq_num>
<VRPTx:pdb_ins_code xsi:nil="true" />
<VRPTx:pdb_mon_id>DC</VRPTx:pdb_mon_id>
<VRPTx:pdb_seq_num>1</VRPTx:pdb_seq_num>
<VRPTx:pdb_strand_id>A</VRPTx:pdb_strand_id>
</VRPTx:pdbx_poly_seq_scheme>
<VRPTx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DG" seq_id="2">
<VRPTx:auth_mon_id>DG</VRPTx:auth_mon_id>
<VRPTx:auth_seq_num>2</VRPTx:auth_seq_num>
<VRPTx:ndb_seq_num>2</VRPTx:ndb_seq_num>
<VRPTx:pdb_ins_code xsi:nil="true" />
<VRPTx:pdb_mon_id>DG</VRPTx:pdb_mon_id>
<VRPTx:pdb_seq_num>2</VRPTx:pdb_seq_num>
<VRPTx:pdb_strand_id>A</VRPTx:pdb_strand_id>
</VRPTx:pdbx_poly_seq_scheme>
<VRPTx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DT" seq_id="3">
<VRPTx:auth_mon_id>DT</VRPTx:auth_mon_id>
<VRPTx:auth_seq_num>3</VRPTx:auth_seq_num>
<VRPTx:ndb_seq_num>3</VRPTx:ndb_seq_num>
<VRPTx:pdb_ins_code xsi:nil="true" />
<VRPTx:pdb_mon_id>DT</VRPTx:pdb_mon_id>
<VRPTx:pdb_seq_num>3</VRPTx:pdb_seq_num>
<VRPTx:pdb_strand_id>A</VRPTx:pdb_strand_id>
</VRPTx:pdbx_poly_seq_scheme>
<VRPTx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DA" seq_id="4">
<VRPTx:auth_mon_id>DA</VRPTx:auth_mon_id>
<VRPTx:auth_seq_num>4</VRPTx:auth_seq_num>
<VRPTx:ndb_seq_num>4</VRPTx:ndb_seq_num>
<VRPTx:pdb_ins_code xsi:nil="true" />
<VRPTx:pdb_mon_id>DA</VRPTx:pdb_mon_id>
<VRPTx:pdb_seq_num>4</VRPTx:pdb_seq_num>
<VRPTx:pdb_strand_id>A</VRPTx:pdb_strand_id>
</VRPTx:pdbx_poly_seq_scheme>
<VRPTx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DC" seq_id="5">
<VRPTx:auth_mon_id>DC</VRPTx:auth_mon_id>
<VRPTx:auth_seq_num>5</VRPTx:auth_seq_num>
<VRPTx:ndb_seq_num>5</VRPTx:ndb_seq_num>
<VRPTx:pdb_ins_code xsi:nil="true" />
<VRPTx:pdb_mon_id>DC</VRPTx:pdb_mon_id>
<VRPTx:pdb_seq_num>5</VRPTx:pdb_seq_num>
<VRPTx:pdb_strand_id>A</VRPTx:pdb_strand_id>
</VRPTx:pdbx_poly_seq_scheme>
<VRPTx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DG" seq_id="6">
<VRPTx:auth_mon_id>DG</VRPTx:auth_mon_id>
<VRPTx:auth_seq_num>6</VRPTx:auth_seq_num>
<VRPTx:ndb_seq_num>6</VRPTx:ndb_seq_num>
<VRPTx:pdb_ins_code xsi:nil="true" />
<VRPTx:pdb_mon_id>DG</VRPTx:pdb_mon_id>
<VRPTx:pdb_seq_num>6</VRPTx:pdb_seq_num>
<VRPTx:pdb_strand_id>A</VRPTx:pdb_strand_id>
</VRPTx:pdbx_poly_seq_scheme>
</VRPTx:pdbx_poly_seq_schemeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_poly_seq_scheme.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_re_refinementType |
|---|---|
| Abstract | no |
| Documentation |
Describes the origin of the experimental data used in this
entry.
Example 1 -
<VRPTx:pdbx_re_refinementCategory>
<VRPTx:pdbx_re_refinement entry_id="1ABC">
<VRPTx:citation_id>2</VRPTx:citation_id>
<VRPTx:details>Re-refinement of data from entry 1ABC</VRPTx:details>
</VRPTx:pdbx_re_refinement>
</VRPTx:pdbx_re_refinementCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_re_refinement.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_refineType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_REFINE category record details about
additional structure refinement parameters which are needed
to complete legacy REMARK 3 refinement templates in PDB
format files.
Example 1 - PDB placeholders for refinement program SHELX
<VRPTx:pdbx_refineCategory>
<VRPTx:pdbx_refine entry_id="ABC001" pdbx_refine_id="x-ray">
<VRPTx:R_factor_all_4sig_cutoff>0.174</VRPTx:R_factor_all_4sig_cutoff>
<VRPTx:R_factor_obs_4sig_cutoff>0.169</VRPTx:R_factor_obs_4sig_cutoff>
<VRPTx:free_R_factor_4sig_cutoff>0.216</VRPTx:free_R_factor_4sig_cutoff>
<VRPTx:free_R_val_test_set_ct_4sig_cutoff>164</VRPTx:free_R_val_test_set_ct_4sig_cutoff>
<VRPTx:free_R_val_test_set_size_perc_4sig_cutoff>1.29</VRPTx:free_R_val_test_set_size_perc_4sig_cutoff>
<VRPTx:number_reflns_obs_4sig_cutoff>1263</VRPTx:number_reflns_obs_4sig_cutoff>
</VRPTx:pdbx_refine>
</VRPTx:pdbx_refineCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_refine.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_refine_componentType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_REFINE_COMPONENT category record
statistics of the final model relative to the density map.
Example 1 -
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_refine_component.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_refine_tlsType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFINE_TLS category record details about
TLS parameters used in structure refinement. Note that the
intention is primarily to describe directly refined TLS
parameters, although other methods of obtaining TLS parameters
may be covered, see item attribute method in category pdbx_refine_tls
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_refine_tls.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_refine_tls_groupType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_REFINE_TLS_GROUP category record details about
a fragment of a TLS group.
Properties of the TLS group are recorded in PDBX_REFINE_TLS
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_refine_tls_group.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_refln_signal_binningType |
|---|---|
| Abstract | no |
| Documentation |
The binning of the per-reflection signal generated by the
software specified by attribute pdbx_signal_software_id.
in category reflns If any reflections have a signal >= to the highest threshold
specified, an additional bin should be inferred to hold them.
Examples 1 - based on an internal STARANISO run
<VRPTx:pdbx_refln_signal_binningCategory>
<VRPTx:pdbx_refln_signal_binning ordinal="1">
<VRPTx:upper_threshold>1.20</VRPTx:upper_threshold>
</VRPTx:pdbx_refln_signal_binning>
<VRPTx:pdbx_refln_signal_binning ordinal="2">
<VRPTx:upper_threshold>7.22</VRPTx:upper_threshold>
</VRPTx:pdbx_refln_signal_binning>
<VRPTx:pdbx_refln_signal_binning ordinal="3">
<VRPTx:upper_threshold>19.00</VRPTx:upper_threshold>
</VRPTx:pdbx_refln_signal_binning>
<VRPTx:pdbx_refln_signal_binning ordinal="4">
<VRPTx:upper_threshold>36.81</VRPTx:upper_threshold>
</VRPTx:pdbx_refln_signal_binning>
<VRPTx:pdbx_refln_signal_binning ordinal="5">
<VRPTx:upper_threshold>48.87</VRPTx:upper_threshold>
</VRPTx:pdbx_refln_signal_binning>
<VRPTx:pdbx_refln_signal_binning ordinal="6">
<VRPTx:upper_threshold>53.84</VRPTx:upper_threshold>
</VRPTx:pdbx_refln_signal_binning>
<VRPTx:pdbx_refln_signal_binning ordinal="7">
<VRPTx:upper_threshold>57.69</VRPTx:upper_threshold>
</VRPTx:pdbx_refln_signal_binning>
</VRPTx:pdbx_refln_signal_binningCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_refln_signal_binning.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_reflns_twinType |
|---|---|
| Abstract | no |
| Documentation |
Details decribing crystallographic twinning.
Example 1 -
<VRPTx:pdbx_reflns_twinCategory>
<VRPTx:pdbx_reflns_twin crystal_id="1" diffrn_id="1" operator="h,-h-k,-l">
<VRPTx:fraction>.43</VRPTx:fraction>
<VRPTx:mean_F_square_over_mean_F2>.84</VRPTx:mean_F_square_over_mean_F2>
<VRPTx:mean_I2_over_mean_I_square>1.3</VRPTx:mean_I2_over_mean_I_square>
<VRPTx:type>merohedral</VRPTx:type>
</VRPTx:pdbx_reflns_twin>
</VRPTx:pdbx_reflns_twinCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_reflns_twin.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_sequence_rangeType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_SEQUENCE_RANGE category identify the
beginning and ending points of polypeptide sequence segments.
Example 1 -
<VRPTx:pdbx_sequence_rangeCategory>
<VRPTx:pdbx_sequence_range beg_label_alt_id="A" beg_label_asym_id="A" beg_label_comp_id="PRO" beg_label_seq_id="1" end_label_alt_id="A" end_label_asym_id="A" end_label_comp_id="GLY" end_label_seq_id="29" seq_range_id="s1"></VRPTx:pdbx_sequence_range>
<VRPTx:pdbx_sequence_range beg_label_alt_id="A" beg_label_asym_id="D" beg_label_comp_id="PRO" beg_label_seq_id="91" end_label_alt_id="A" end_label_asym_id="D" end_label_comp_id="GLY" end_label_seq_id="119" seq_range_id="s2"></VRPTx:pdbx_sequence_range>
</VRPTx:pdbx_sequence_rangeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_sequence_range.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_sifts_unp_segmentsType |
|---|---|
| Abstract | no |
| Documentation |
pdbx_sifts_unp_segments describes residue-range based cross-references specific to UniProt.
Example 1 -
<VRPTx:pdbx_sifts_unp_segmentsCategory>
<VRPTx:pdbx_sifts_unp_segments asym_id="A" entity_id="1" instance_id="1" segment_id="1" unp_acc="A0A5J6CYR6">
<VRPTx:best_mapping>Y</VRPTx:best_mapping>
<VRPTx:identity>0.95</VRPTx:identity>
<VRPTx:seq_id_end>260</VRPTx:seq_id_end>
<VRPTx:seq_id_start>26</VRPTx:seq_id_start>
<VRPTx:unp_end>238</VRPTx:unp_end>
<VRPTx:unp_start>2</VRPTx:unp_start>
</VRPTx:pdbx_sifts_unp_segments>
</VRPTx:pdbx_sifts_unp_segmentsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_sifts_unp_segments.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_sifts_xref_dbType |
|---|---|
| Abstract | no |
| Documentation |
pdbx_sifts_xref_db describes residue-level cross-references to external databases.
Example 1 -
<VRPTx:pdbx_sifts_xref_dbCategory>
<VRPTx:pdbx_sifts_xref_db asym_id="A" entity_id="1" seq_id="254" seq_id_ordinal="1">
<VRPTx:mh_id>1</VRPTx:mh_id>
<VRPTx:mon_id>ILE</VRPTx:mon_id>
<VRPTx:mon_id_one_letter_code>I</VRPTx:mon_id_one_letter_code>
<VRPTx:observed>1</VRPTx:observed>
<VRPTx:res_type xsi:nil="true" />
<VRPTx:unp_acc>P00720</VRPTx:unp_acc>
<VRPTx:unp_instance_id>1</VRPTx:unp_instance_id>
<VRPTx:unp_num>50</VRPTx:unp_num>
<VRPTx:unp_res>I</VRPTx:unp_res>
<VRPTx:unp_segment_id>1</VRPTx:unp_segment_id>
<VRPTx:xref_db_acc>PF14843</VRPTx:xref_db_acc>
<VRPTx:xref_db_instance_id>1</VRPTx:xref_db_instance_id>
<VRPTx:xref_db_name>Pfam</VRPTx:xref_db_name>
<VRPTx:xref_db_segment_id>1</VRPTx:xref_db_segment_id>
<VRPTx:xref_domain_name xsi:nil="true" />
</VRPTx:pdbx_sifts_xref_db>
</VRPTx:pdbx_sifts_xref_dbCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_sifts_xref_db.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_sifts_xref_db_segmentsType |
|---|---|
| Abstract | no |
| Documentation |
pdbx_sifts_xref_db_segments describes residue-range based cross-references to external databases.
Example 1 -
<VRPTx:pdbx_sifts_xref_db_segmentsCategory>
<VRPTx:pdbx_sifts_xref_db_segments asym_id="A" entity_id="1" instance_id="1" segment_id="1" seq_id_end="252" seq_id_start="26" xref_db="SCOP2B" xref_db_acc="8102030">
<VRPTx:domain_name>SF</VRPTx:domain_name>
</VRPTx:pdbx_sifts_xref_db_segments>
</VRPTx:pdbx_sifts_xref_db_segmentsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_sifts_xref_db_segments.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_soln_scatterType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_SOLN_SCATTER category record details about a
solution scattering experiment
Example 1 - based on PDB entry 1HAQ
<VRPTx:pdbx_soln_scatterCategory>
<VRPTx:pdbx_soln_scatter entry_id="1HAQ" id="1">
<VRPTx:buffer_name>tris</VRPTx:buffer_name>
<VRPTx:concentration_range>0.7 - 14</VRPTx:concentration_range>
<VRPTx:detector_specific xsi:nil="true" />
<VRPTx:detector_type>500-channel quadrant</VRPTx:detector_type>
<VRPTx:max_mean_cross_sectional_radii_gyration>1.7</VRPTx:max_mean_cross_sectional_radii_gyration>
<VRPTx:max_mean_cross_sectional_radii_gyration_esd>0.1</VRPTx:max_mean_cross_sectional_radii_gyration_esd>
<VRPTx:mean_guiner_radius>11.1</VRPTx:mean_guiner_radius>
<VRPTx:mean_guiner_radius_esd>0.4</VRPTx:mean_guiner_radius_esd>
<VRPTx:min_mean_cross_sectional_radii_gyration>4.4</VRPTx:min_mean_cross_sectional_radii_gyration>
<VRPTx:min_mean_cross_sectional_radii_gyration_esd>0.2</VRPTx:min_mean_cross_sectional_radii_gyration_esd>
<VRPTx:num_time_frames>10</VRPTx:num_time_frames>
<VRPTx:protein_length>40</VRPTx:protein_length>
<VRPTx:sample_pH xsi:nil="true" />
<VRPTx:source_beamline>2.1</VRPTx:source_beamline>
<VRPTx:source_beamline_instrument xsi:nil="true" />
<VRPTx:source_class>synchrotron</VRPTx:source_class>
<VRPTx:source_type>SRS BEAMLINE 2.1</VRPTx:source_type>
<VRPTx:temperature>288</VRPTx:temperature>
<VRPTx:type>x-ray</VRPTx:type>
</VRPTx:pdbx_soln_scatter>
<VRPTx:pdbx_soln_scatter entry_id="1HAQ" id="2">
<VRPTx:buffer_name>PBS in 99.9% D2O</VRPTx:buffer_name>
<VRPTx:concentration_range>0.4 - 9.6</VRPTx:concentration_range>
<VRPTx:detector_specific xsi:nil="true" />
<VRPTx:detector_type>area</VRPTx:detector_type>
<VRPTx:max_mean_cross_sectional_radii_gyration>1.51</VRPTx:max_mean_cross_sectional_radii_gyration>
<VRPTx:max_mean_cross_sectional_radii_gyration_esd>0.06</VRPTx:max_mean_cross_sectional_radii_gyration_esd>
<VRPTx:mean_guiner_radius>11.3</VRPTx:mean_guiner_radius>
<VRPTx:mean_guiner_radius_esd>0.4</VRPTx:mean_guiner_radius_esd>
<VRPTx:min_mean_cross_sectional_radii_gyration>3.9</VRPTx:min_mean_cross_sectional_radii_gyration>
<VRPTx:min_mean_cross_sectional_radii_gyration_esd>0.2</VRPTx:min_mean_cross_sectional_radii_gyration_esd>
<VRPTx:num_time_frames xsi:nil="true" />
<VRPTx:protein_length>37.0 - 39.0</VRPTx:protein_length>
<VRPTx:sample_pH xsi:nil="true" />
<VRPTx:source_beamline xsi:nil="true" />
<VRPTx:source_beamline_instrument>D11, D22</VRPTx:source_beamline_instrument>
<VRPTx:source_class>neutron source</VRPTx:source_class>
<VRPTx:source_type>ILL</VRPTx:source_type>
<VRPTx:temperature xsi:nil="true" />
<VRPTx:type>neutron</VRPTx:type>
</VRPTx:pdbx_soln_scatter>
<VRPTx:pdbx_soln_scatter entry_id="1HAQ" id="3">
<VRPTx:buffer_name>PBS in 99.9% D2O</VRPTx:buffer_name>
<VRPTx:concentration_range>3.7, 6.1</VRPTx:concentration_range>
<VRPTx:detector_specific xsi:nil="true" />
<VRPTx:detector_type>AREA (TIME-OF-FLIGHT)</VRPTx:detector_type>
<VRPTx:max_mean_cross_sectional_radii_gyration xsi:nil="true" />
<VRPTx:max_mean_cross_sectional_radii_gyration_esd xsi:nil="true" />
<VRPTx:mean_guiner_radius>11.7</VRPTx:mean_guiner_radius>
<VRPTx:mean_guiner_radius_esd>0.5</VRPTx:mean_guiner_radius_esd>
<VRPTx:min_mean_cross_sectional_radii_gyration xsi:nil="true" />
<VRPTx:min_mean_cross_sectional_radii_gyration_esd xsi:nil="true" />
<VRPTx:num_time_frames xsi:nil="true" />
<VRPTx:protein_length>40.0</VRPTx:protein_length>
<VRPTx:sample_pH xsi:nil="true" />
<VRPTx:source_beamline>Pulsed Neutron</VRPTx:source_beamline>
<VRPTx:source_beamline_instrument>LOQ</VRPTx:source_beamline_instrument>
<VRPTx:source_class>neutron source</VRPTx:source_class>
<VRPTx:source_type>ISIS</VRPTx:source_type>
<VRPTx:temperature xsi:nil="true" />
<VRPTx:type>neutron</VRPTx:type>
</VRPTx:pdbx_soln_scatter>
</VRPTx:pdbx_soln_scatterCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_soln_scatter.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_soln_scatter_modelType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_SOLN_SCATTER_MODEL category record details about the
homology model fitting to the solution scatter data.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_soln_scatter_model.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_assemblyType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_ASSEMBLY category record details about
the structural elements that form macromolecular assemblies.
Example 1 -
<VRPTx:pdbx_struct_assemblyCategory>
<VRPTx:pdbx_struct_assembly id="1">
<VRPTx:details> The icosahedral virus particle.</VRPTx:details>
</VRPTx:pdbx_struct_assembly>
</VRPTx:pdbx_struct_assemblyCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_assembly.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_assembly_genType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_ASSEMBLY_GEN category record details about
the generation of each macromolecular assemblies. The PDBX_STRUCT_ASSEMBLY_GEN
data items provide the specifications of the components that
constitute that assembly in terms of cartesian transformations.
Example 1 -
<VRPTx:pdbx_struct_assembly_genCategory>
<VRPTx:pdbx_struct_assembly_gen assembly_id="1" asym_id_list="A" oper_expression="1"></VRPTx:pdbx_struct_assembly_gen>
<VRPTx:pdbx_struct_assembly_gen assembly_id="1" asym_id_list="B" oper_expression="1"></VRPTx:pdbx_struct_assembly_gen>
<VRPTx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="A" oper_expression="2"></VRPTx:pdbx_struct_assembly_gen>
<VRPTx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="B" oper_expression="2"></VRPTx:pdbx_struct_assembly_gen>
<VRPTx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="C" oper_expression="2"></VRPTx:pdbx_struct_assembly_gen>
<VRPTx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="A" oper_expression="3"></VRPTx:pdbx_struct_assembly_gen>
<VRPTx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="B" oper_expression="3"></VRPTx:pdbx_struct_assembly_gen>
<VRPTx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="D" oper_expression="3"></VRPTx:pdbx_struct_assembly_gen>
</VRPTx:pdbx_struct_assembly_genCategory>
Example 2 -
<VRPTx:pdbx_struct_assembly_genCategory>
<VRPTx:pdbx_struct_assembly_gen assembly_id="1" asym_id_list="A,B" oper_expression="1"></VRPTx:pdbx_struct_assembly_gen>
<VRPTx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="A,B,C" oper_expression="2"></VRPTx:pdbx_struct_assembly_gen>
<VRPTx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="A,B,D" oper_expression="3"></VRPTx:pdbx_struct_assembly_gen>
</VRPTx:pdbx_struct_assembly_genCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_assembly_gen.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_assembly_propType |
|---|---|
| Abstract | no |
| Documentation |
Properties and features of structural assemblies.
Example 1 -
<VRPTx:pdbx_struct_assembly_propCategory>
<VRPTx:pdbx_struct_assembly_prop biol_id="1" type="ABSA">
<VRPTx:details> </VRPTx:details>
<VRPTx:value>1456.7</VRPTx:value>
</VRPTx:pdbx_struct_assembly_prop>
</VRPTx:pdbx_struct_assembly_propCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_assembly_prop.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_asym_genType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_ASYM_GEN category record details about
the generation of the crystallographic asymmetric unit. The
PDBX_STRUCT_ASYM_GEN data items provide the specifications of the
components that constitute the asymmetric unit in terms of cartesian
transformations of deposited coordinates.
Example 1 -
<VRPTx:pdbx_struct_asym_genCategory>
<VRPTx:pdbx_struct_asym_gen entity_inst_id="A" oper_expression="1">
<VRPTx:asym_id>A</VRPTx:asym_id>
</VRPTx:pdbx_struct_asym_gen>
<VRPTx:pdbx_struct_asym_gen entity_inst_id="B" oper_expression="1">
<VRPTx:asym_id>B</VRPTx:asym_id>
</VRPTx:pdbx_struct_asym_gen>
</VRPTx:pdbx_struct_asym_genCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_asym_gen.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_chem_comp_diagnosticsType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_CHEM_COMP_DIAGNOSTICS category provides
structural diagnostics in chemical components instances.
Example 1 -
<VRPTx:pdbx_struct_chem_comp_diagnosticsCategory>
<VRPTx:pdbx_struct_chem_comp_diagnostics ordinal="1">
<VRPTx:asym_id>Q</VRPTx:asym_id>
<VRPTx:auth_comp_id>Q20</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>10</VRPTx:auth_seq_id>
<VRPTx:details>Strained geometry. Long carbonyl bond at C10.</VRPTx:details>
<VRPTx:pdb_strand_id>Q</VRPTx:pdb_strand_id>
<VRPTx:seq_num xsi:nil="true" />
<VRPTx:type>GEOMETRY</VRPTx:type>
</VRPTx:pdbx_struct_chem_comp_diagnostics>
</VRPTx:pdbx_struct_chem_comp_diagnosticsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_chem_comp_diagnostics.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_conn_angleType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_CONN_ANGLE category record the angles
in connections between portions of the structure.
Example 1 - PDB entry 2v8d
<VRPTx:pdbx_struct_conn_angleCategory>
<VRPTx:pdbx_struct_conn_angle id="1">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>114</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>104.7</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="2">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>226</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>91.3</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="3">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>114</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>226</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>120.6</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="4">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>2041</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>172.5</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="5">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>114</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>2041</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>80.0</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="6">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>226</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>2041</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>91.3</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="7">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>3001</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>76.9</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="8">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>114</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>3001</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>112.3</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="9">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>226</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>3001</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>127.0</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="10">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>O</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>HOH</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>2041</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>3001</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>95.9</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="11">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>OE</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>GLU</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>160</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>89.8</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="12">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>3001</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>95.5</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="13">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>OE</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>GLU</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>160</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>O</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HOH</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>3001</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>109.4</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="14">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>421</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>90.4</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="15">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>OE</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>GLU</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>160</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>421</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>111.3</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="16">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>O</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>HOH</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>3001</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>A</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>421</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>138.9</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="17">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>O</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>HOH</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>3001</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>114</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>106.4</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="18">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>O</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>HOH</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>3001</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>OD</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>ASP</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>125</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>100.5</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="19">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>114</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>OD</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>ASP</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>125</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>115.6</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="20">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>O</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>HOH</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>3001</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>226</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>123.2</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="21">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>NE</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>HIS</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>114</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>226</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>123.2</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="22">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>OD</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>ASP</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>125</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>500</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>NE</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>HIS</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>226</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>82.7</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
<VRPTx:pdbx_struct_conn_angle id="23">
<VRPTx:ptnr1_PDB_ins_code xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>OE</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>GLU</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>160</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr2_PDB_ins_code>ZN</VRPTx:ptnr2_PDB_ins_code>
<VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id xsi:nil="true" />
<VRPTx:ptnr2_label_comp_id>ZN</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>501</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr3_PDB_ins_code>OD</VRPTx:ptnr3_PDB_ins_code>
<VRPTx:ptnr3_label_asym_id>B</VRPTx:ptnr3_label_asym_id>
<VRPTx:ptnr3_label_atom_id xsi:nil="true" />
<VRPTx:ptnr3_label_comp_id>ASP</VRPTx:ptnr3_label_comp_id>
<VRPTx:ptnr3_label_seq_id>125</VRPTx:ptnr3_label_seq_id>
<VRPTx:value>148.6</VRPTx:value>
</VRPTx:pdbx_struct_conn_angle>
</VRPTx:pdbx_struct_conn_angleCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_conn_angle.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_entity_instType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_ENTITY_INST category record details about the
structural elements in the deposited entry. The entity instance is a method
neutral identifier for the observed molecular entities in the deposited coordinate
set.
Example 1 -
<VRPTx:pdbx_struct_entity_instCategory>
<VRPTx:pdbx_struct_entity_inst id="A">
<VRPTx:details>one monomer of the dimeric enzyme</VRPTx:details>
<VRPTx:entity_id>1</VRPTx:entity_id>
</VRPTx:pdbx_struct_entity_inst>
<VRPTx:pdbx_struct_entity_inst id="B">
<VRPTx:details>one monomer of the dimeric enzyme</VRPTx:details>
<VRPTx:entity_id>1</VRPTx:entity_id>
</VRPTx:pdbx_struct_entity_inst>
</VRPTx:pdbx_struct_entity_instCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_entity_inst.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_group_component_rangeType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_GROUP_COMPONENT_RANGE category define a structural
group as a continuous span chemical components.
Example 1 -
<VRPTx:pdbx_struct_group_component_rangeCategory>
<VRPTx:pdbx_struct_group_component_range ordinal="1">
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:beg_PDB_ins_code xsi:nil="true" />
<VRPTx:beg_auth_asym_id>A</VRPTx:beg_auth_asym_id>
<VRPTx:beg_auth_comp_id>MLU</VRPTx:beg_auth_comp_id>
<VRPTx:beg_auth_seq_id>1</VRPTx:beg_auth_seq_id>
<VRPTx:end_PDB_ins_code xsi:nil="true" />
<VRPTx:end_auth_asym_id>A</VRPTx:end_auth_asym_id>
<VRPTx:end_auth_comp_id>RAM</VRPTx:end_auth_comp_id>
<VRPTx:end_auth_seq_id>10</VRPTx:end_auth_seq_id>
<VRPTx:struct_group_id>1</VRPTx:struct_group_id>
</VRPTx:pdbx_struct_group_component_range>
</VRPTx:pdbx_struct_group_component_rangeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_group_component_range.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_group_componentsType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_GROUP_COMPONENTS category list component-level
group assignments within the entry. Groups are defined and described in category
PDBX_STRUCT_GROUP_LIST.
Example 1 -
<VRPTx:pdbx_struct_group_componentsCategory>
<VRPTx:pdbx_struct_group_components ordinal="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>MLU</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>1</VRPTx:auth_seq_id>
<VRPTx:struct_group_id>1</VRPTx:struct_group_id>
</VRPTx:pdbx_struct_group_components>
<VRPTx:pdbx_struct_group_components ordinal="2">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>OMZ</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>2</VRPTx:auth_seq_id>
<VRPTx:struct_group_id>1</VRPTx:struct_group_id>
</VRPTx:pdbx_struct_group_components>
<VRPTx:pdbx_struct_group_components ordinal="3">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>ASN</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:struct_group_id>1</VRPTx:struct_group_id>
</VRPTx:pdbx_struct_group_components>
<VRPTx:pdbx_struct_group_components ordinal="4">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>GHP</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>4</VRPTx:auth_seq_id>
<VRPTx:struct_group_id>1</VRPTx:struct_group_id>
</VRPTx:pdbx_struct_group_components>
<VRPTx:pdbx_struct_group_components ordinal="5">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>GHP</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>5</VRPTx:auth_seq_id>
<VRPTx:struct_group_id>1</VRPTx:struct_group_id>
</VRPTx:pdbx_struct_group_components>
<VRPTx:pdbx_struct_group_components ordinal="6">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>OMX</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>6</VRPTx:auth_seq_id>
<VRPTx:struct_group_id>1</VRPTx:struct_group_id>
</VRPTx:pdbx_struct_group_components>
<VRPTx:pdbx_struct_group_components ordinal="7">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>3FG</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>7</VRPTx:auth_seq_id>
<VRPTx:struct_group_id>1</VRPTx:struct_group_id>
</VRPTx:pdbx_struct_group_components>
<VRPTx:pdbx_struct_group_components ordinal="8">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>ERE</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>8</VRPTx:auth_seq_id>
<VRPTx:struct_group_id>1</VRPTx:struct_group_id>
</VRPTx:pdbx_struct_group_components>
<VRPTx:pdbx_struct_group_components ordinal="9">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>BGC</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>9</VRPTx:auth_seq_id>
<VRPTx:struct_group_id>1</VRPTx:struct_group_id>
</VRPTx:pdbx_struct_group_components>
<VRPTx:pdbx_struct_group_components ordinal="10">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>RAM</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>10</VRPTx:auth_seq_id>
<VRPTx:struct_group_id>1</VRPTx:struct_group_id>
</VRPTx:pdbx_struct_group_components>
</VRPTx:pdbx_struct_group_componentsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_group_components.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_group_listType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_GROUP_LIST define groups of related components
or atoms.
Example 1 -
<VRPTx:pdbx_struct_group_listCategory>
<VRPTx:pdbx_struct_group_list struct_group_id="1">
<VRPTx:description> Decaplanin is a tricyclic glycopeptide. The scaffold is a heptapeptide with the
configuration D-D-L-D-D-L-L, glycosylated by a monosaccharide and a disaccharide</VRPTx:description>
<VRPTx:group_enumeration_type>component</VRPTx:group_enumeration_type>
<VRPTx:name>DECAPLANIN</VRPTx:name>
<VRPTx:type>MolecularComplex</VRPTx:type>
</VRPTx:pdbx_struct_group_list>
</VRPTx:pdbx_struct_group_listCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_group_list.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_infoType |
|---|---|
| Abstract | no |
| Documentation |
Special features of this structural entry.
Example 1 -
<VRPTx:pdbx_struct_infoCategory>
<VRPTx:pdbx_struct_info type="nonpolymer_zero_occupancy_flag" value="Y"></VRPTx:pdbx_struct_info>
<VRPTx:pdbx_struct_info type="polymer_zero_occupancy_flag" value="Y"></VRPTx:pdbx_struct_info>
<VRPTx:pdbx_struct_info type="multiple_model_flag" value="Y"></VRPTx:pdbx_struct_info>
<VRPTx:pdbx_struct_info type="multiple_model_details" value="Model 3 missing ligand ACX"></VRPTx:pdbx_struct_info>
<VRPTx:pdbx_struct_info type="nonpolymer_details" value="Disordered ligand geometry for C34 with missing pyridine ring"></VRPTx:pdbx_struct_info>
<VRPTx:pdbx_struct_info type="missing atoms in alternate conformations" value="Y"></VRPTx:pdbx_struct_info>
</VRPTx:pdbx_struct_infoCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_info.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_legacy_oper_listType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_LEGACY_OPER_LIST category describe
Cartesian rotation and translation operations required to
generate or transform the coordinates deposited with this entry.
This category provides a container for matrices used to construct
icosahedral assemblies in legacy entries.
Example 1 -
<VRPTx:pdbx_struct_legacy_oper_listCategory>
<VRPTx:pdbx_struct_legacy_oper_list id="2">
<VRPTx:matrix11>0.247</VRPTx:matrix11>
<VRPTx:matrix12>0.935</VRPTx:matrix12>
<VRPTx:matrix13>0.256</VRPTx:matrix13>
<VRPTx:matrix21>0.929</VRPTx:matrix21>
<VRPTx:matrix22>0.153</VRPTx:matrix22>
<VRPTx:matrix23>0.337</VRPTx:matrix23>
<VRPTx:matrix31>0.276</VRPTx:matrix31>
<VRPTx:matrix32>0.321</VRPTx:matrix32>
<VRPTx:matrix33>-0.906</VRPTx:matrix33>
<VRPTx:vector1>-8.253</VRPTx:vector1>
<VRPTx:vector2>-11.743</VRPTx:vector2>
<VRPTx:vector3>-1.782</VRPTx:vector3>
</VRPTx:pdbx_struct_legacy_oper_list>
</VRPTx:pdbx_struct_legacy_oper_listCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_legacy_oper_list.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_mod_residueType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_MOD_RESIDUE category list the
modified polymer components in the entry and provide some
details describing the nature of the modification.
Example 1 -
<VRPTx:pdbx_struct_mod_residueCategory>
<VRPTx:pdbx_struct_mod_residue id="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>CRW</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>66</VRPTx:auth_seq_id>
<VRPTx:details>CIRCULARIZED TRI-PEPTIDE CHROMOPHORE</VRPTx:details>
<VRPTx:parent_comp_id>ALA</VRPTx:parent_comp_id>
</VRPTx:pdbx_struct_mod_residue>
<VRPTx:pdbx_struct_mod_residue id="2">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>CRW</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>66</VRPTx:auth_seq_id>
<VRPTx:details>CIRCULARIZED TRI-PEPTIDE CHROMOPHORE</VRPTx:details>
<VRPTx:parent_comp_id>SER</VRPTx:parent_comp_id>
</VRPTx:pdbx_struct_mod_residue>
<VRPTx:pdbx_struct_mod_residue id="3">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>CRW</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>66</VRPTx:auth_seq_id>
<VRPTx:details>CIRCULARIZED TRI-PEPTIDE CHROMOPHORE</VRPTx:details>
<VRPTx:parent_comp_id>GLY</VRPTx:parent_comp_id>
</VRPTx:pdbx_struct_mod_residue>
</VRPTx:pdbx_struct_mod_residueCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_mod_residue.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_msym_genType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_MSYM_GEN category record details about
the generation of the minimal asymmetric unit. For instance, this
category can be used to provide this information for helical and point
symmetry systems. The PDBX_STRUCT_MSYM_GEN data items provide the
specifications of the components that constitute the asymmetric unit
in terms of cartesian transformations of deposited coordinates.
Example 1 -
<VRPTx:pdbx_struct_msym_genCategory>
<VRPTx:pdbx_struct_msym_gen entity_inst_id="A" msym_id="A" oper_expression="3"></VRPTx:pdbx_struct_msym_gen>
<VRPTx:pdbx_struct_msym_gen entity_inst_id="B" msym_id="B" oper_expression="4"></VRPTx:pdbx_struct_msym_gen>
<VRPTx:pdbx_struct_msym_gen entity_inst_id="B" msym_id="C" oper_expression="5"></VRPTx:pdbx_struct_msym_gen>
</VRPTx:pdbx_struct_msym_genCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_msym_gen.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_nmr_ens_clustType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_STRUCT_NMR_ENS_CLUST category record information about cluster analysis of the NMR ensemble structure. Example 1 - <VRPTx:pdbx_struct_nmr_ens_clustCategory> <VRPTx:pdbx_struct_nmr_ens_clust entry_id="5UB9"> <VRPTx:clusters_total_number>4</VRPTx:clusters_total_number> <VRPTx:conformers_total_number>20</VRPTx:conformers_total_number> <VRPTx:error>success</VRPTx:error> <VRPTx:outliers_total_number>2</VRPTx:outliers_total_number> </VRPTx:pdbx_struct_nmr_ens_clust> </VRPTx:pdbx_struct_nmr_ens_clustCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_nmr_ens_clust_genType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_STRUCT_NMR_ENS_CLUST_GEN category records generation of clusters (group of conformers) by cluster analysis of the NMR ensemble structure. Example 1 - <VRPTx:pdbx_struct_nmr_ens_clust_genCategory> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="1"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="2"> <VRPTx:cluster_id>3</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="3"> <VRPTx:cluster_id>2</VRPTx:cluster_id> <VRPTx:medoid_conformer>Y</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="4"> <VRPTx:cluster_id>3</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="5"> <VRPTx:cluster_id>2</VRPTx:cluster_id> <VRPTx:medoid_conformer>Y</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="6"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="7"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="8"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="9"> <VRPTx:cluster_id>outlier</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="10"> <VRPTx:cluster_id>2</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="11"> <VRPTx:cluster_id>2</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="12"> <VRPTx:cluster_id>2</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="13"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>Y</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="14"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="15"> <VRPTx:cluster_id>2</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="16"> <VRPTx:cluster_id>1</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="17"> <VRPTx:cluster_id>4</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="18"> <VRPTx:cluster_id>3</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="19"> <VRPTx:cluster_id>outlier</VRPTx:cluster_id> <VRPTx:medoid_conformer>N</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> <VRPTx:pdbx_struct_nmr_ens_clust_gen PDB_model_num="20"> <VRPTx:cluster_id>4</VRPTx:cluster_id> <VRPTx:medoid_conformer>Y</VRPTx:medoid_conformer> </VRPTx:pdbx_struct_nmr_ens_clust_gen> </VRPTx:pdbx_struct_nmr_ens_clust_genCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_nmr_ens_domType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_STRUCT_NMR_ENS_DOM category records generation of domains (polypeptide chain segments) by domain identification of the NMR ensemble structure. Example 1 - <VRPTx:pdbx_struct_nmr_ens_domCategory> <VRPTx:pdbx_struct_nmr_ens_dom id="1"> <VRPTx:distance_rms_dev>0.800</VRPTx:distance_rms_dev> <VRPTx:distance_rms_dev_medoid>0.652</VRPTx:distance_rms_dev_medoid> <VRPTx:error>success</VRPTx:error> <VRPTx:medoid_model_number>3</VRPTx:medoid_model_number> <VRPTx:number_of_gaps>2</VRPTx:number_of_gaps> <VRPTx:number_of_monomers>96</VRPTx:number_of_monomers> </VRPTx:pdbx_struct_nmr_ens_dom> </VRPTx:pdbx_struct_nmr_ens_domCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_nmr_ens_dom_limType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_STRUCT_NMR_ENS_DOM_LIM category identify the start and end points of generated polypeptide chain segments (domains) of the NMR ensemble structure. Example 1 - <VRPTx:pdbx_struct_nmr_ens_dom_limCategory> <VRPTx:pdbx_struct_nmr_ens_dom_lim component_id="1" dom_id="1"> <VRPTx:beg_auth_asym_id>A</VRPTx:beg_auth_asym_id> <VRPTx:beg_auth_comp_id>THR</VRPTx:beg_auth_comp_id> <VRPTx:beg_auth_seq_id>515</VRPTx:beg_auth_seq_id> <VRPTx:end_auth_asym_id>A</VRPTx:end_auth_asym_id> <VRPTx:end_auth_comp_id>THR</VRPTx:end_auth_comp_id> <VRPTx:end_auth_seq_id>525</VRPTx:end_auth_seq_id> </VRPTx:pdbx_struct_nmr_ens_dom_lim> <VRPTx:pdbx_struct_nmr_ens_dom_lim component_id="2" dom_id="1"> <VRPTx:beg_auth_asym_id>A</VRPTx:beg_auth_asym_id> <VRPTx:beg_auth_comp_id>ASN</VRPTx:beg_auth_comp_id> <VRPTx:beg_auth_seq_id>530</VRPTx:beg_auth_seq_id> <VRPTx:end_auth_asym_id>A</VRPTx:end_auth_asym_id> <VRPTx:end_auth_comp_id>LYS</VRPTx:end_auth_comp_id> <VRPTx:end_auth_seq_id>555</VRPTx:end_auth_seq_id> </VRPTx:pdbx_struct_nmr_ens_dom_lim> <VRPTx:pdbx_struct_nmr_ens_dom_lim component_id="3" dom_id="1"> <VRPTx:beg_auth_asym_id>A</VRPTx:beg_auth_asym_id> <VRPTx:beg_auth_comp_id>ASP</VRPTx:beg_auth_comp_id> <VRPTx:beg_auth_seq_id>560</VRPTx:beg_auth_seq_id> <VRPTx:end_auth_asym_id>A</VRPTx:end_auth_asym_id> <VRPTx:end_auth_comp_id>ARG</VRPTx:end_auth_comp_id> <VRPTx:end_auth_seq_id>616</VRPTx:end_auth_seq_id> </VRPTx:pdbx_struct_nmr_ens_dom_lim> </VRPTx:pdbx_struct_nmr_ens_dom_limCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_oper_listType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_OPER_LIST category describe
Cartesian rotation and translation operations required to
generate or transform the coordinates deposited with this entry.
Example 1 -
<VRPTx:pdbx_struct_oper_listCategory>
<VRPTx:pdbx_struct_oper_list id="2">
<VRPTx:matrix11>0.247</VRPTx:matrix11>
<VRPTx:matrix12>0.935</VRPTx:matrix12>
<VRPTx:matrix13>0.256</VRPTx:matrix13>
<VRPTx:matrix21>0.929</VRPTx:matrix21>
<VRPTx:matrix22>0.153</VRPTx:matrix22>
<VRPTx:matrix23>0.337</VRPTx:matrix23>
<VRPTx:matrix31>0.276</VRPTx:matrix31>
<VRPTx:matrix32>0.321</VRPTx:matrix32>
<VRPTx:matrix33>-0.906</VRPTx:matrix33>
<VRPTx:type>point symmetry operation</VRPTx:type>
<VRPTx:vector1>-8.253</VRPTx:vector1>
<VRPTx:vector2>-11.743</VRPTx:vector2>
<VRPTx:vector3>-1.782</VRPTx:vector3>
</VRPTx:pdbx_struct_oper_list>
</VRPTx:pdbx_struct_oper_listCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_oper_list.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_ref_seq_deletionType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category
annotate deletions in the sequence of the entity described
in the referenced database entry.
Example 1 -
<VRPTx:pdbx_struct_ref_seq_deletionCategory>
<VRPTx:pdbx_struct_ref_seq_deletion id="1">
<VRPTx:asym_id>A</VRPTx:asym_id>
<VRPTx:comp_id>LEU</VRPTx:comp_id>
<VRPTx:db_code>P15456</VRPTx:db_code>
<VRPTx:db_name>UNP</VRPTx:db_name>
<VRPTx:db_seq_id>23</VRPTx:db_seq_id>
<VRPTx:details xsi:nil="true" />
</VRPTx:pdbx_struct_ref_seq_deletion>
<VRPTx:pdbx_struct_ref_seq_deletion id="1">
<VRPTx:asym_id>A</VRPTx:asym_id>
<VRPTx:comp_id>THR</VRPTx:comp_id>
<VRPTx:db_code>P15456</VRPTx:db_code>
<VRPTx:db_name>UNP</VRPTx:db_name>
<VRPTx:db_seq_id>24</VRPTx:db_seq_id>
<VRPTx:details xsi:nil="true" />
</VRPTx:pdbx_struct_ref_seq_deletion>
<VRPTx:pdbx_struct_ref_seq_deletion id="1">
<VRPTx:asym_id>A</VRPTx:asym_id>
<VRPTx:comp_id>GLN</VRPTx:comp_id>
<VRPTx:db_code>P15456</VRPTx:db_code>
<VRPTx:db_name>UNP</VRPTx:db_name>
<VRPTx:db_seq_id>25</VRPTx:db_seq_id>
<VRPTx:details xsi:nil="true" />
</VRPTx:pdbx_struct_ref_seq_deletion>
</VRPTx:pdbx_struct_ref_seq_deletionCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_ref_seq_deletion.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_ref_seq_insertionType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category
annotate insertions in the sequence of the entity described
in the referenced database entry.
Example 1 -
<VRPTx:pdbx_struct_ref_seq_insertionCategory>
<VRPTx:pdbx_struct_ref_seq_insertion id="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:asym_id>A</VRPTx:asym_id>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_seq_id>104</VRPTx:auth_seq_id>
<VRPTx:comp_id>GLY</VRPTx:comp_id>
<VRPTx:db_code>P00752</VRPTx:db_code>
<VRPTx:db_name>UNP</VRPTx:db_name>
<VRPTx:details>INSERTION</VRPTx:details>
<VRPTx:seq_id>102</VRPTx:seq_id>
</VRPTx:pdbx_struct_ref_seq_insertion>
<VRPTx:pdbx_struct_ref_seq_insertion id="2">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:asym_id>A</VRPTx:asym_id>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_seq_id>105</VRPTx:auth_seq_id>
<VRPTx:comp_id>TRP</VRPTx:comp_id>
<VRPTx:db_code>P00752</VRPTx:db_code>
<VRPTx:db_name>UNP</VRPTx:db_name>
<VRPTx:details>INSERTION</VRPTx:details>
<VRPTx:seq_id>103</VRPTx:seq_id>
</VRPTx:pdbx_struct_ref_seq_insertion>
</VRPTx:pdbx_struct_ref_seq_insertionCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_ref_seq_insertion.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_sheet_hbondType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_SHEET_HBOND category record details
about the hydrogen bonding between residue ranges in a beta sheet.
This category is provided for cases where only a single hydrogen
bond is used to register the two residue ranges. Category
STRUCT_SHEET_HBOND should be used when the initial and terminal
hydrogen bonds for strand pair are known.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_sheet_hbond.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_struct_special_symmetryType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_STRUCT_SPECIAL_SYMMETRY category list the
molecular components that lie on special symmetry positions.
Example 1 -
<VRPTx:pdbx_struct_special_symmetryCategory>
<VRPTx:pdbx_struct_special_symmetry id="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>Q</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>ATP</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>412</VRPTx:auth_seq_id>
<VRPTx:label_alt_id xsi:nil="true" />
</VRPTx:pdbx_struct_special_symmetry>
</VRPTx:pdbx_struct_special_symmetryCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_special_symmetry.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_unobs_or_zero_occ_atomsType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_UNOBS_OR_ZERO_OCC_ATOMS category list the
atoms within the entry that are either unobserved or have zero occupancy/
Example 1 -
<VRPTx:pdbx_unobs_or_zero_occ_atomsCategory>
<VRPTx:pdbx_unobs_or_zero_occ_atoms id="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>CG</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>412</VRPTx:auth_seq_id>
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:occupancy_flag>1</VRPTx:occupancy_flag>
<VRPTx:polymer_flag>Y</VRPTx:polymer_flag>
</VRPTx:pdbx_unobs_or_zero_occ_atoms>
<VRPTx:pdbx_unobs_or_zero_occ_atoms id="2">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>CD</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>412</VRPTx:auth_seq_id>
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:occupancy_flag>1</VRPTx:occupancy_flag>
<VRPTx:polymer_flag>Y</VRPTx:polymer_flag>
</VRPTx:pdbx_unobs_or_zero_occ_atoms>
<VRPTx:pdbx_unobs_or_zero_occ_atoms id="3">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>NE</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>412</VRPTx:auth_seq_id>
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:occupancy_flag>1</VRPTx:occupancy_flag>
<VRPTx:polymer_flag>Y</VRPTx:polymer_flag>
</VRPTx:pdbx_unobs_or_zero_occ_atoms>
<VRPTx:pdbx_unobs_or_zero_occ_atoms id="4">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>CZ</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>412</VRPTx:auth_seq_id>
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:occupancy_flag>1</VRPTx:occupancy_flag>
<VRPTx:polymer_flag>Y</VRPTx:polymer_flag>
</VRPTx:pdbx_unobs_or_zero_occ_atoms>
<VRPTx:pdbx_unobs_or_zero_occ_atoms id="5">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>NH1</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>412</VRPTx:auth_seq_id>
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:occupancy_flag>1</VRPTx:occupancy_flag>
<VRPTx:polymer_flag>Y</VRPTx:polymer_flag>
</VRPTx:pdbx_unobs_or_zero_occ_atoms>
<VRPTx:pdbx_unobs_or_zero_occ_atoms id="6">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>NH2</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>412</VRPTx:auth_seq_id>
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:occupancy_flag>1</VRPTx:occupancy_flag>
<VRPTx:polymer_flag>Y</VRPTx:polymer_flag>
</VRPTx:pdbx_unobs_or_zero_occ_atoms>
</VRPTx:pdbx_unobs_or_zero_occ_atomsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_unobs_or_zero_occ_atoms.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_unobs_or_zero_occ_residuesType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES category list the
residues within the entry that are not observed or have zero occupancy.
Example 1 -
<VRPTx:pdbx_unobs_or_zero_occ_residuesCategory>
<VRPTx:pdbx_unobs_or_zero_occ_residues id="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>B</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>VAL</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>36</VRPTx:auth_seq_id>
<VRPTx:occupancy_flag>1</VRPTx:occupancy_flag>
<VRPTx:polymer_flag>Y</VRPTx:polymer_flag>
</VRPTx:pdbx_unobs_or_zero_occ_residues>
<VRPTx:pdbx_unobs_or_zero_occ_residues id="2">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>B</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>ARG</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>108</VRPTx:auth_seq_id>
<VRPTx:occupancy_flag>1</VRPTx:occupancy_flag>
<VRPTx:polymer_flag>Y</VRPTx:polymer_flag>
</VRPTx:pdbx_unobs_or_zero_occ_residues>
<VRPTx:pdbx_unobs_or_zero_occ_residues id="3">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>D</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>PPI</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>438</VRPTx:auth_seq_id>
<VRPTx:occupancy_flag>1</VRPTx:occupancy_flag>
<VRPTx:polymer_flag>N</VRPTx:polymer_flag>
</VRPTx:pdbx_unobs_or_zero_occ_residues>
</VRPTx:pdbx_unobs_or_zero_occ_residuesCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_unobs_or_zero_occ_residues.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_chiralType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_VALIDATE_CHIRAL category list the
residues that contain unexpected configuration of chiral
centers.
IMPROPER HA N C CB chirality CA
IMPROPER HB1 HB2 CA CG stereo CB
as this number approaches (+) or (-) 180.0, then the
error in predicting the true chirality of the center increases.
Improper dihedrals are a measure of the chirality/planarity of the
structure at a specific atom. Values around -35 or +35 are expected
for chiral atoms, and values around 0 for planar atoms.
HERE improper C---N----CA---CB done
expected answer is around -120 mean -122.52
D-amino acid is +120.0
Example 1 -
<VRPTx:pdbx_validate_chiralCategory>
<VRPTx:pdbx_validate_chiral id="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>0</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>ASP</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>B</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>405</VRPTx:auth_seq_id>
<VRPTx:details>ALPHA-CARBON</VRPTx:details>
<VRPTx:omega>150.48</VRPTx:omega>
</VRPTx:pdbx_validate_chiral>
</VRPTx:pdbx_validate_chiralCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_validate_chiral.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_close_contactType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_VALIDATE_CLOSE_CONTACT category list the
atoms within the entry that are in close contact with regard
the distances expected from either covalent bonding or closest
approach by van der Waals contacts. Contacts within
the asymmetric unit are considered.
For those contacts not involving hydrogen a limit of
2.2 angstroms is used. For contacts involving a hydrogen atom
a cutoff of 1.6 angstroms is used.
Example 1 -
<VRPTx:pdbx_validate_close_contactCategory>
<VRPTx:pdbx_validate_close_contact id="1">
<VRPTx:PDB_ins_code_1 xsi:nil="true" />
<VRPTx:PDB_ins_code_2 xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id_1>B</VRPTx:auth_asym_id_1>
<VRPTx:auth_asym_id_2>B</VRPTx:auth_asym_id_2>
<VRPTx:auth_atom_id_1 xsi:nil="true" />
<VRPTx:auth_atom_id_2 xsi:nil="true" />
<VRPTx:auth_comp_id_1>VAL</VRPTx:auth_comp_id_1>
<VRPTx:auth_comp_id_2>ARG</VRPTx:auth_comp_id_2>
<VRPTx:auth_seq_id_1>36</VRPTx:auth_seq_id_1>
<VRPTx:auth_seq_id_2>108</VRPTx:auth_seq_id_2>
<VRPTx:dist>2.16</VRPTx:dist>
<VRPTx:label_alt_id_1 xsi:nil="true" />
<VRPTx:label_alt_id_2 xsi:nil="true" />
</VRPTx:pdbx_validate_close_contact>
<VRPTx:pdbx_validate_close_contact id="2">
<VRPTx:PDB_ins_code_1 xsi:nil="true" />
<VRPTx:PDB_ins_code_2 xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id_1>B</VRPTx:auth_asym_id_1>
<VRPTx:auth_asym_id_2>B</VRPTx:auth_asym_id_2>
<VRPTx:auth_atom_id_1 xsi:nil="true" />
<VRPTx:auth_atom_id_2 xsi:nil="true" />
<VRPTx:auth_comp_id_1>ARG</VRPTx:auth_comp_id_1>
<VRPTx:auth_comp_id_2>VAL</VRPTx:auth_comp_id_2>
<VRPTx:auth_seq_id_1>108</VRPTx:auth_seq_id_1>
<VRPTx:auth_seq_id_2>36</VRPTx:auth_seq_id_2>
<VRPTx:dist>2.16</VRPTx:dist>
<VRPTx:label_alt_id_1 xsi:nil="true" />
<VRPTx:label_alt_id_2 xsi:nil="true" />
</VRPTx:pdbx_validate_close_contact>
</VRPTx:pdbx_validate_close_contactCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_validate_close_contact.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_main_chain_planeType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_VALIDATE_MAIN_CHAIN_PLANE category list the
residues that contain unexpected deviations from planes
for main chain atoms as defined by the improper torsion
angle describing planarity:
PLANARITY = C(i-1) - CA(i-1) - N(i) - O(i-1) ==> planar < 5
as a pseudo torsion
Example 1 -
<VRPTx:pdbx_validate_main_chain_planeCategory>
<VRPTx:pdbx_validate_main_chain_plane id="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>0</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>G</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>TRP</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>20</VRPTx:auth_seq_id>
<VRPTx:improper_torsion_angle>29.901</VRPTx:improper_torsion_angle>
</VRPTx:pdbx_validate_main_chain_plane>
<VRPTx:pdbx_validate_main_chain_plane id="2">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>0</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>G</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>TRP</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>21</VRPTx:auth_seq_id>
<VRPTx:improper_torsion_angle>-42.450</VRPTx:improper_torsion_angle>
</VRPTx:pdbx_validate_main_chain_plane>
</VRPTx:pdbx_validate_main_chain_planeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_validate_main_chain_plane.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_nmr_chem_shiftType |
|---|---|
| Abstract | no |
| Documentation | Items in the PDBX_VALIDATE_NMR_CHEM_SHIFT category provide information about assigned chemical shifts that deviate from expected BMRB standards by 5 * the expected RMSD. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_peptide_omegaType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_VALIDATE_PEPTIDE_OMEGA category list the
residues that contain peptide bonds deviate
significantly from both cis and trans conformation.
cis bonds, if any, are listed on cispep records.
trans is defined as 180 +/- 30 and
cis is defined as 0 +/- 30 degrees.
Example 1 -
<VRPTx:pdbx_validate_peptide_omegaCategory>
<VRPTx:pdbx_validate_peptide_omega id="1">
<VRPTx:PDB_ins_code_1 xsi:nil="true" />
<VRPTx:PDB_ins_code_2 xsi:nil="true" />
<VRPTx:PDB_model_num>0</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id_1>ASP</VRPTx:auth_asym_id_1>
<VRPTx:auth_asym_id_2>ARG</VRPTx:auth_asym_id_2>
<VRPTx:auth_comp_id_1>A</VRPTx:auth_comp_id_1>
<VRPTx:auth_comp_id_2>A</VRPTx:auth_comp_id_2>
<VRPTx:auth_seq_id_1>414</VRPTx:auth_seq_id_1>
<VRPTx:auth_seq_id_2>413</VRPTx:auth_seq_id_2>
<VRPTx:label_alt_id_1 xsi:nil="true" />
<VRPTx:label_alt_id_2 xsi:nil="true" />
<VRPTx:omega>147.84</VRPTx:omega>
</VRPTx:pdbx_validate_peptide_omega>
<VRPTx:pdbx_validate_peptide_omega id="2">
<VRPTx:PDB_ins_code_1 xsi:nil="true" />
<VRPTx:PDB_ins_code_2 xsi:nil="true" />
<VRPTx:PDB_model_num>0</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id_1>ASN</VRPTx:auth_asym_id_1>
<VRPTx:auth_asym_id_2>ALA</VRPTx:auth_asym_id_2>
<VRPTx:auth_comp_id_1>B</VRPTx:auth_comp_id_1>
<VRPTx:auth_comp_id_2>B</VRPTx:auth_comp_id_2>
<VRPTx:auth_seq_id_1>289</VRPTx:auth_seq_id_1>
<VRPTx:auth_seq_id_2>288</VRPTx:auth_seq_id_2>
<VRPTx:label_alt_id_1 xsi:nil="true" />
<VRPTx:label_alt_id_2 xsi:nil="true" />
<VRPTx:omega>-39.12</VRPTx:omega>
</VRPTx:pdbx_validate_peptide_omega>
</VRPTx:pdbx_validate_peptide_omegaCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_validate_peptide_omega.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_planesType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_VALIDATE_PLANES category list the
residues that contain unexpected deviations from planes
centers.
Example 1 -
<VRPTx:pdbx_validate_planesCategory>
<VRPTx:pdbx_validate_planes id="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>DG</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:rmsd>0.068</VRPTx:rmsd>
<VRPTx:type>SIDE CHAIN</VRPTx:type>
</VRPTx:pdbx_validate_planes>
<VRPTx:pdbx_validate_planes id="2">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>DT</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>4</VRPTx:auth_seq_id>
<VRPTx:rmsd>0.198</VRPTx:rmsd>
<VRPTx:type>SIDE CHAIN</VRPTx:type>
</VRPTx:pdbx_validate_planes>
<VRPTx:pdbx_validate_planes id="3">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>DC</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>8</VRPTx:auth_seq_id>
<VRPTx:rmsd>0.090</VRPTx:rmsd>
<VRPTx:type>SIDE CHAIN</VRPTx:type>
</VRPTx:pdbx_validate_planes>
</VRPTx:pdbx_validate_planesCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_validate_planes.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_planes_atomType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_VALIDATE_PLANES_ATOM category list the
residues that contain unexpected deviations from planes
centers.
Example 1 -
<VRPTx:pdbx_validate_planes_atomCategory>
<VRPTx:pdbx_validate_planes_atom id="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.003</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>N1</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:plane_id>1</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
<VRPTx:pdbx_validate_planes_atom id="2">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.011</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>C2</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:plane_id>1</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
<VRPTx:pdbx_validate_planes_atom id="3">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.074</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>N2</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:plane_id>1</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
<VRPTx:pdbx_validate_planes_atom id="4">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.005</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>N3</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:plane_id>1</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
<VRPTx:pdbx_validate_planes_atom id="5">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.010</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>C4</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:plane_id>1</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
<VRPTx:pdbx_validate_planes_atom id="6">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.029</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>C5</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:plane_id>1</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
<VRPTx:pdbx_validate_planes_atom id="7">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.039</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>C6</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:plane_id>1</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
<VRPTx:pdbx_validate_planes_atom id="8">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.074</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>O6</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:plane_id>1</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
<VRPTx:pdbx_validate_planes_atom id="9">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.050</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>N7</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:plane_id>1</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
<VRPTx:pdbx_validate_planes_atom id="10">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.129</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>C8</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:plane_id>1</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
<VRPTx:pdbx_validate_planes_atom id="11">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.033</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>N9</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:plane_id>1</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
<VRPTx:pdbx_validate_planes_atom id="12">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.147</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DG</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>C1'</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>3</VRPTx:auth_seq_id>
<VRPTx:plane_id>1</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
<VRPTx:pdbx_validate_planes_atom id="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:atom_deviation>0.069</VRPTx:atom_deviation>
<VRPTx:auth_asym_id>DT</VRPTx:auth_asym_id>
<VRPTx:auth_atom_id>N1</VRPTx:auth_atom_id>
<VRPTx:auth_comp_id>A</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>4</VRPTx:auth_seq_id>
<VRPTx:plane_id>2</VRPTx:plane_id>
</VRPTx:pdbx_validate_planes_atom>
</VRPTx:pdbx_validate_planes_atomCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_validate_planes_atom.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_polymer_linkageType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_VALIDATE_POLYMER_LINKAGE category list the
polymer linkages within the entry that are outside of typical
covalent distances.
Example 1 -
<VRPTx:pdbx_validate_polymer_linkageCategory>
<VRPTx:pdbx_validate_polymer_linkage id="1">
<VRPTx:PDB_ins_code_1 xsi:nil="true" />
<VRPTx:PDB_ins_code_2 xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id_1>B</VRPTx:auth_asym_id_1>
<VRPTx:auth_asym_id_2>B</VRPTx:auth_asym_id_2>
<VRPTx:auth_atom_id_1 xsi:nil="true" />
<VRPTx:auth_atom_id_2 xsi:nil="true" />
<VRPTx:auth_comp_id_1>VAL</VRPTx:auth_comp_id_1>
<VRPTx:auth_comp_id_2>ARG</VRPTx:auth_comp_id_2>
<VRPTx:auth_seq_id_1>107</VRPTx:auth_seq_id_1>
<VRPTx:auth_seq_id_2>108</VRPTx:auth_seq_id_2>
<VRPTx:dist>3.16</VRPTx:dist>
<VRPTx:label_alt_id_1 xsi:nil="true" />
<VRPTx:label_alt_id_2 xsi:nil="true" />
</VRPTx:pdbx_validate_polymer_linkage>
<VRPTx:pdbx_validate_polymer_linkage id="2">
<VRPTx:PDB_ins_code_1 xsi:nil="true" />
<VRPTx:PDB_ins_code_2 xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id_1>B</VRPTx:auth_asym_id_1>
<VRPTx:auth_asym_id_2>B</VRPTx:auth_asym_id_2>
<VRPTx:auth_atom_id_1 xsi:nil="true" />
<VRPTx:auth_atom_id_2 xsi:nil="true" />
<VRPTx:auth_comp_id_1>ARG</VRPTx:auth_comp_id_1>
<VRPTx:auth_comp_id_2>LYS</VRPTx:auth_comp_id_2>
<VRPTx:auth_seq_id_1>110</VRPTx:auth_seq_id_1>
<VRPTx:auth_seq_id_2>110</VRPTx:auth_seq_id_2>
<VRPTx:dist>2.95</VRPTx:dist>
<VRPTx:label_alt_id_1 xsi:nil="true" />
<VRPTx:label_alt_id_2 xsi:nil="true" />
</VRPTx:pdbx_validate_polymer_linkage>
</VRPTx:pdbx_validate_polymer_linkageCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_validate_polymer_linkage.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_rmsd_angleType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_VALIDATE_RMSD_ANGLE category list
the covalent bond angles found in an entry that have
values which deviate from expected values by more
than 6*rmsd for the particular entry from the expected standard
value
Example 1 -
<VRPTx:pdbx_validate_rmsd_angleCategory>
<VRPTx:pdbx_validate_rmsd_angle id="1">
<VRPTx:PDB_ins_code_1 xsi:nil="true" />
<VRPTx:PDB_ins_code_2 xsi:nil="true" />
<VRPTx:PDB_ins_code_3 xsi:nil="true" />
<VRPTx:PDB_model_num>0</VRPTx:PDB_model_num>
<VRPTx:angle_deviation>-3.14</VRPTx:angle_deviation>
<VRPTx:angle_value>117.16</VRPTx:angle_value>
<VRPTx:auth_asym_id_1>A</VRPTx:auth_asym_id_1>
<VRPTx:auth_asym_id_2>A</VRPTx:auth_asym_id_2>
<VRPTx:auth_asym_id_3>A</VRPTx:auth_asym_id_3>
<VRPTx:auth_atom_id_1>NE</VRPTx:auth_atom_id_1>
<VRPTx:auth_atom_id_2>CZ</VRPTx:auth_atom_id_2>
<VRPTx:auth_atom_id_3>NH2</VRPTx:auth_atom_id_3>
<VRPTx:auth_comp_id_1>ARG</VRPTx:auth_comp_id_1>
<VRPTx:auth_comp_id_2>ARG</VRPTx:auth_comp_id_2>
<VRPTx:auth_comp_id_3>ARG</VRPTx:auth_comp_id_3>
<VRPTx:auth_seq_id_1>35</VRPTx:auth_seq_id_1>
<VRPTx:auth_seq_id_2>35</VRPTx:auth_seq_id_2>
<VRPTx:auth_seq_id_3>35</VRPTx:auth_seq_id_3>
<VRPTx:label_alt_id_1 xsi:nil="true" />
<VRPTx:label_alt_id_2 xsi:nil="true" />
<VRPTx:label_alt_id_3 xsi:nil="true" />
<VRPTx:linker_flag>N</VRPTx:linker_flag>
</VRPTx:pdbx_validate_rmsd_angle>
<VRPTx:pdbx_validate_rmsd_angle id="2">
<VRPTx:PDB_ins_code_1 xsi:nil="true" />
<VRPTx:PDB_ins_code_2 xsi:nil="true" />
<VRPTx:PDB_ins_code_3 xsi:nil="true" />
<VRPTx:PDB_model_num>0</VRPTx:PDB_model_num>
<VRPTx:angle_deviation>34.68</VRPTx:angle_deviation>
<VRPTx:angle_value>148.88</VRPTx:angle_value>
<VRPTx:auth_asym_id_1>A</VRPTx:auth_asym_id_1>
<VRPTx:auth_asym_id_2>A</VRPTx:auth_asym_id_2>
<VRPTx:auth_asym_id_3>A</VRPTx:auth_asym_id_3>
<VRPTx:auth_atom_id_1>CB</VRPTx:auth_atom_id_1>
<VRPTx:auth_atom_id_2>CG</VRPTx:auth_atom_id_2>
<VRPTx:auth_atom_id_3>CD</VRPTx:auth_atom_id_3>
<VRPTx:auth_comp_id_1>GLU</VRPTx:auth_comp_id_1>
<VRPTx:auth_comp_id_2>GLU</VRPTx:auth_comp_id_2>
<VRPTx:auth_comp_id_3>GLU</VRPTx:auth_comp_id_3>
<VRPTx:auth_seq_id_1>166</VRPTx:auth_seq_id_1>
<VRPTx:auth_seq_id_2>166</VRPTx:auth_seq_id_2>
<VRPTx:auth_seq_id_3>166</VRPTx:auth_seq_id_3>
<VRPTx:label_alt_id_1 xsi:nil="true" />
<VRPTx:label_alt_id_2 xsi:nil="true" />
<VRPTx:label_alt_id_3 xsi:nil="true" />
<VRPTx:linker_flag>N</VRPTx:linker_flag>
</VRPTx:pdbx_validate_rmsd_angle>
</VRPTx:pdbx_validate_rmsd_angleCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_validate_rmsd_angle.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_rmsd_bondType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_VALIDATE_RMSD_BOND category list the
covalent bonds that have values which deviate from expected
values by more than 6*rmsd.
Example 1 -
<VRPTx:pdbx_validate_rmsd_bondCategory>
<VRPTx:pdbx_validate_rmsd_bond id="1">
<VRPTx:PDB_ins_code_1 xsi:nil="true" />
<VRPTx:PDB_ins_code_2 xsi:nil="true" />
<VRPTx:PDB_model_num>0</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id_1>A</VRPTx:auth_asym_id_1>
<VRPTx:auth_asym_id_2>A</VRPTx:auth_asym_id_2>
<VRPTx:auth_atom_id_1>CD</VRPTx:auth_atom_id_1>
<VRPTx:auth_atom_id_2>CE</VRPTx:auth_atom_id_2>
<VRPTx:auth_comp_id_1>LYS</VRPTx:auth_comp_id_1>
<VRPTx:auth_comp_id_2>LYS</VRPTx:auth_comp_id_2>
<VRPTx:auth_seq_id_1>152</VRPTx:auth_seq_id_1>
<VRPTx:auth_seq_id_2>152</VRPTx:auth_seq_id_2>
<VRPTx:bond_deviation>-0.372</VRPTx:bond_deviation>
<VRPTx:bond_value>1.136</VRPTx:bond_value>
<VRPTx:label_alt_id_1 xsi:nil="true" />
<VRPTx:label_alt_id_2 xsi:nil="true" />
<VRPTx:linker_flag>N</VRPTx:linker_flag>
</VRPTx:pdbx_validate_rmsd_bond>
<VRPTx:pdbx_validate_rmsd_bond id="2">
<VRPTx:PDB_ins_code_1 xsi:nil="true" />
<VRPTx:PDB_ins_code_2 xsi:nil="true" />
<VRPTx:PDB_model_num>0</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id_1>A</VRPTx:auth_asym_id_1>
<VRPTx:auth_asym_id_2>A</VRPTx:auth_asym_id_2>
<VRPTx:auth_atom_id_1>CG</VRPTx:auth_atom_id_1>
<VRPTx:auth_atom_id_2>CD</VRPTx:auth_atom_id_2>
<VRPTx:auth_comp_id_1>GLU</VRPTx:auth_comp_id_1>
<VRPTx:auth_comp_id_2>GLU</VRPTx:auth_comp_id_2>
<VRPTx:auth_seq_id_1>166</VRPTx:auth_seq_id_1>
<VRPTx:auth_seq_id_2>166</VRPTx:auth_seq_id_2>
<VRPTx:bond_deviation>-0.622</VRPTx:bond_deviation>
<VRPTx:bond_value>0.893</VRPTx:bond_value>
<VRPTx:label_alt_id_1 xsi:nil="true" />
<VRPTx:label_alt_id_2 xsi:nil="true" />
<VRPTx:linker_flag>N</VRPTx:linker_flag>
</VRPTx:pdbx_validate_rmsd_bond>
</VRPTx:pdbx_validate_rmsd_bondCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_validate_rmsd_bond.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_rmsd_ringType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_VALIDATE_RMSD_RING category list the residues that contain unexpected deviations of dihedral angles in a ring conformation. The values are computed by Mogul. Mogul finds the similar ring conformations from small-molecule structures in the Cambridge Structural Database (CSD). Example 1 - <VRPTx:pdbx_validate_rmsd_ringCategory> <VRPTx:pdbx_validate_rmsd_ring id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> <VRPTx:dihedral_angle_standard_deviation>5.62</VRPTx:dihedral_angle_standard_deviation> <VRPTx:dihedral_angle_target_value>73.11</VRPTx:dihedral_angle_target_value> </VRPTx:pdbx_validate_rmsd_ring> <VRPTx:pdbx_validate_rmsd_ring id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> <VRPTx:dihedral_angle_standard_deviation>6.08</VRPTx:dihedral_angle_standard_deviation> <VRPTx:dihedral_angle_target_value>74.52</VRPTx:dihedral_angle_target_value> </VRPTx:pdbx_validate_rmsd_ring> </VRPTx:pdbx_validate_rmsd_ringCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_rmsd_rings_atomType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_VALIDATE_RMSD_RINGS_ATOM category list the atoms involved in outlier ring conformations instanced in the PDBX_VALIDATE_RMSD_RING category. The values are computed by Mogul. Mogul finds the similar ring conformations from small-molecule structures in the Cambridge Structural Database (CSD). Example 1 - <VRPTx:pdbx_validate_rmsd_rings_atomCategory> <VRPTx:pdbx_validate_rmsd_rings_atom id="1" ring_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C1</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="2" ring_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C2</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="3" ring_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C3</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="4" ring_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="5" ring_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C5</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="6" ring_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C6</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="1" ring_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C1</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="2" ring_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C2</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="3" ring_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C3</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="4" ring_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="5" ring_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C5</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> <VRPTx:pdbx_validate_rmsd_rings_atom id="6" ring_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C6</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_rings_atom> </VRPTx:pdbx_validate_rmsd_rings_atomCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_rmsd_torsionType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_VALIDATE_RMSD_TORSION category list the residues that contain unexpected deviations of torsion angles. The values are computed by Mogul. Mogul finds the similar conformations from small-molecule structures in the Cambridge Structural Database (CSD). Example 1 - <VRPTx:pdbx_validate_rmsd_torsionCategory> <VRPTx:pdbx_validate_rmsd_torsion id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> <VRPTx:dihedral_angle_standard_deviation>5.62</VRPTx:dihedral_angle_standard_deviation> <VRPTx:dihedral_angle_target_value>73.11</VRPTx:dihedral_angle_target_value> </VRPTx:pdbx_validate_rmsd_torsion> <VRPTx:pdbx_validate_rmsd_torsion id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> <VRPTx:dihedral_angle_standard_deviation>6.08</VRPTx:dihedral_angle_standard_deviation> <VRPTx:dihedral_angle_target_value>74.52</VRPTx:dihedral_angle_target_value> </VRPTx:pdbx_validate_rmsd_torsion> </VRPTx:pdbx_validate_rmsd_torsionCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_rmsd_torsions_atomType |
|---|---|
| Abstract | no |
| Documentation | Data items in the PDBX_VALIDATE_RMSD_TORSIONS_ATOM category list the atoms involved in outlier conformations instanced in the PDBX_VALIDATE_RMSD_TORSION category. The values are computed by Mogul. Mogul finds the similar conformations from small-molecule structures in the Cambridge Structural Database (CSD). Example 1 - <VRPTx:pdbx_validate_rmsd_torsions_atomCategory> <VRPTx:pdbx_validate_rmsd_torsions_atom id="1" torsion_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C1</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="2" torsion_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C2</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="3" torsion_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C3</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="4" torsion_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="5" torsion_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C5</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="6" torsion_id="1"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>A</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C6</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="1" torsion_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C1</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="2" torsion_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C2</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="3" torsion_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C3</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="4" torsion_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="5" torsion_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C5</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> <VRPTx:pdbx_validate_rmsd_torsions_atom id="6" torsion_id="2"> <VRPTx:PDB_ins_code xsi:nil="true" /> <VRPTx:PDB_model_num>1</VRPTx:PDB_model_num> <VRPTx:auth_asym_id>B</VRPTx:auth_asym_id> <VRPTx:auth_atom_id>C6</VRPTx:auth_atom_id> <VRPTx:auth_comp_id>BBA</VRPTx:auth_comp_id> <VRPTx:auth_seq_id>250</VRPTx:auth_seq_id> </VRPTx:pdbx_validate_rmsd_torsions_atom> </VRPTx:pdbx_validate_rmsd_torsions_atomCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_symm_contactType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_VALIDATE_SYMM_CONTACT category list the
atoms within the entry that are in close contact with regard
the distances expected from either covalent bonding or closest
approach by van der Waals contacts. Contacts with
for symmetry related contacts are considered.
For those contacts not involving hydrogen a limit of
2.2 angstroms is used. For contacts involving a hydrogen atom
a cutoff of 1.6 angstrom is used.
Example 1 -
<VRPTx:pdbx_validate_symm_contactCategory>
<VRPTx:pdbx_validate_symm_contact id="1">
<VRPTx:PDB_ins_code_1 xsi:nil="true" />
<VRPTx:PDB_ins_code_2 xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id_1 xsi:nil="true" />
<VRPTx:auth_asym_id_2 xsi:nil="true" />
<VRPTx:auth_atom_id_1>O</VRPTx:auth_atom_id_1>
<VRPTx:auth_atom_id_2>O</VRPTx:auth_atom_id_2>
<VRPTx:auth_comp_id_1>HOH</VRPTx:auth_comp_id_1>
<VRPTx:auth_comp_id_2>HOH</VRPTx:auth_comp_id_2>
<VRPTx:auth_seq_id_1>70</VRPTx:auth_seq_id_1>
<VRPTx:auth_seq_id_2>70</VRPTx:auth_seq_id_2>
<VRPTx:dist>2.05</VRPTx:dist>
<VRPTx:label_alt_id_1 xsi:nil="true" />
<VRPTx:label_alt_id_2 xsi:nil="true" />
<VRPTx:site_symmetry_1>1555</VRPTx:site_symmetry_1>
<VRPTx:site_symmetry_2>7555</VRPTx:site_symmetry_2>
</VRPTx:pdbx_validate_symm_contact>
</VRPTx:pdbx_validate_symm_contactCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_validate_symm_contact.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validate_torsionType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PDBX_VALIDATE_TORSION category list the
residues with torsion angles outside the expected Ramachandran regions
Example 1 -
<VRPTx:pdbx_validate_torsionCategory>
<VRPTx:pdbx_validate_torsion id="1">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>SER</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>12</VRPTx:auth_seq_id>
<VRPTx:phi>-64.75</VRPTx:phi>
<VRPTx:psi>2.02</VRPTx:psi>
</VRPTx:pdbx_validate_torsion>
<VRPTx:pdbx_validate_torsion id="2">
<VRPTx:PDB_ins_code xsi:nil="true" />
<VRPTx:PDB_model_num>1</VRPTx:PDB_model_num>
<VRPTx:auth_asym_id>A</VRPTx:auth_asym_id>
<VRPTx:auth_comp_id>THR</VRPTx:auth_comp_id>
<VRPTx:auth_seq_id>22</VRPTx:auth_seq_id>
<VRPTx:phi>-116.30</VRPTx:phi>
<VRPTx:psi>61.44</VRPTx:psi>
</VRPTx:pdbx_validate_torsion>
</VRPTx:pdbx_validate_torsionCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_validate_torsion.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | pdbx_validation_softwareType |
|---|---|
| Abstract | no |
| Documentation | Description of the software that was used for wwPDB validation pipeline. The description should include the name of the software and the version used. This example describes the software used in wwPDB validation pipeline. <VRPTx:pdbx_validation_softwareCategory> <VRPTx:pdbx_validation_software ordinal="1"> <VRPTx:classification>refinement package</VRPTx:classification> <VRPTx:details xsi:nil="true" /> <VRPTx:name>EDS</VRPTx:name> <VRPTx:version>trunk28620</VRPTx:version> </VRPTx:pdbx_validation_software> <VRPTx:pdbx_validation_software ordinal="2"> <VRPTx:classification>refinement package</VRPTx:classification> <VRPTx:details xsi:nil="true" /> <VRPTx:name>DCC</VRPTx:name> <VRPTx:version>2.18 (2016-06-28)</VRPTx:version> </VRPTx:pdbx_validation_software> <VRPTx:pdbx_validation_software ordinal="3"> <VRPTx:classification>geometric validation</VRPTx:classification> <VRPTx:details xsi:nil="true" /> <VRPTx:name>Mogul</VRPTx:name> <VRPTx:version>1.7.2 (RC1), CSD as538be (2017)</VRPTx:version> </VRPTx:pdbx_validation_software> <VRPTx:pdbx_validation_software ordinal="4"> <VRPTx:classification>phasing,refinement</VRPTx:classification> <VRPTx:details xsi:nil="true" /> <VRPTx:name>Xtriage</VRPTx:name> <VRPTx:version>1.9-1692</VRPTx:version> </VRPTx:pdbx_validation_software> </VRPTx:pdbx_validation_softwareCategory> |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasingType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING category record details about the
phasing of the structure, listing the various methods used in
the phasing process. Details about the application of each
method are listed in the appropriate subcategories.
Example 1 - hypothetical example.
<VRPTx:phasingCategory>
<VRPTx:phasing method="mir"></VRPTx:phasing>
<VRPTx:phasing method="averaging"></VRPTx:phasing>
</VRPTx:phasingCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_MADType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_MAD category record details about
the phasing of the structure where methods involving
multiple-wavelength anomalous-dispersion techniques are involved.
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
<VRPTx:phasing_MADCategory>
<VRPTx:phasing_MAD entry_id="NCAD"></VRPTx:phasing_MAD>
</VRPTx:phasing_MADCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_MAD.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_MAD_clustType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_MAD_CLUST category record details
about a cluster of experiments that contributed to the
generation of a set of phases.
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
<VRPTx:phasing_MAD_clustCategory>
<VRPTx:phasing_MAD_clust expt_id="1" id="4 wavelength">
<VRPTx:number_set>4</VRPTx:number_set>
</VRPTx:phasing_MAD_clust>
<VRPTx:phasing_MAD_clust expt_id="1" id="5 wavelength">
<VRPTx:number_set>5</VRPTx:number_set>
</VRPTx:phasing_MAD_clust>
<VRPTx:phasing_MAD_clust expt_id="2" id="5 wavelength">
<VRPTx:number_set>5</VRPTx:number_set>
</VRPTx:phasing_MAD_clust>
</VRPTx:phasing_MAD_clustCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_MAD_clust.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_MAD_exptType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_MAD_EXPT category record details about
a MAD phasing experiment, such as the number of experiments that
were clustered together to produce a set of phases or the
statistics for those phases.
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
<VRPTx:phasing_MAD_exptCategory>
<VRPTx:phasing_MAD_expt id="1">
<VRPTx:R_normal_all>0.063</VRPTx:R_normal_all>
<VRPTx:R_normal_anom_scat>0.451</VRPTx:R_normal_anom_scat>
<VRPTx:delta_delta_phi>58.5</VRPTx:delta_delta_phi>
<VRPTx:delta_phi_sigma>20.3</VRPTx:delta_phi_sigma>
<VRPTx:mean_fom>0.88</VRPTx:mean_fom>
<VRPTx:number_clust>2</VRPTx:number_clust>
</VRPTx:phasing_MAD_expt>
<VRPTx:phasing_MAD_expt id="2">
<VRPTx:R_normal_all>0.051</VRPTx:R_normal_all>
<VRPTx:R_normal_anom_scat>0.419</VRPTx:R_normal_anom_scat>
<VRPTx:delta_delta_phi>36.8</VRPTx:delta_delta_phi>
<VRPTx:delta_phi_sigma>18.2</VRPTx:delta_phi_sigma>
<VRPTx:mean_fom>0.93</VRPTx:mean_fom>
<VRPTx:number_clust>1</VRPTx:number_clust>
</VRPTx:phasing_MAD_expt>
</VRPTx:phasing_MAD_exptCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_MAD_expt.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_MAD_ratioType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_MAD_RATIO category record
the ratios of phasing statistics between pairs of data sets
in a MAD phasing experiment, in given shells of resolution.
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
<VRPTx:phasing_MAD_ratioCategory>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.4013">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.084</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.076</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3857">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.067</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3852">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.051</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3847">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.044</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.110</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.049</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.049</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.067</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.149</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.072</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.039</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.102</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.071</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.4013">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.114</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.111</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3857">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.089</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3852">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.086</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3847">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.077</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.140</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.127</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.085</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.089</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.155</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.119</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.082</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.124</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.120</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.075</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.027</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.041</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.060</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3784">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.057</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.2862">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.072</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.105</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.032</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.036</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3784">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.044</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.2862">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.065</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.072</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.031</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3784">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.040</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.2862">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.059</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.3784">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.059</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.032</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.2862">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.059</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.2862" wavelength_2="1.3847">
<VRPTx:d_res_high>4.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.058</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.028</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.078</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.075</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.059</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.067</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3784">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.084</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.2862">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.073</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.101</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.088</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.066</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3784">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.082</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.2862">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.085</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.097</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.074</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3784">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.081</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.2862">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.085</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.3784">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.114</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.089</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.2862">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.103</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.2862" wavelength_2="1.2862">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>4.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.062</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.060</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7263">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.035</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.026</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7251">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.028</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7284">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.023</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7246">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.025</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7217">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.026</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7251">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.060</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.026</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7284">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.029</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7246">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.031</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7217">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.035</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7284">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.075</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.030</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7246">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.023</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7217">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.027</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7246">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.069</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.026</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7217">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.024</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7217" wavelength_2="0.7284">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.060</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.028</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7263">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.060</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.050</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7251">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.056</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7284">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.055</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7246">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.053</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7217">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.056</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7251">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.089</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.050</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7284">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.054</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7246">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.058</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7217">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.063</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7284">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.104</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.057</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7246">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.052</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7217">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.057</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7246">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.098</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.052</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7217">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl xsi:nil="true" />
<VRPTx:ratio_one_wl_centric xsi:nil="true" />
<VRPTx:ratio_two_wl>0.054</VRPTx:ratio_two_wl>
</VRPTx:phasing_MAD_ratio>
<VRPTx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7217" wavelength_2="0.7284">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>3.00</VRPTx:d_res_low>
<VRPTx:ratio_one_wl>0.089</VRPTx:ratio_one_wl>
<VRPTx:ratio_one_wl_centric>0.060</VRPTx:ratio_one_wl_centric>
<VRPTx:ratio_two_wl xsi:nil="true" />
</VRPTx:phasing_MAD_ratio>
</VRPTx:phasing_MAD_ratioCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_MAD_ratio.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_MAD_setType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_MAD_SET category record
details about the individual data sets used in a MAD phasing
experiment.
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
<VRPTx:phasing_MAD_setCategory>
<VRPTx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="aa" wavelength="1.4013">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>3.80</VRPTx:f_double_prime>
<VRPTx:f_prime>-12.48</VRPTx:f_prime>
<VRPTx:wavelength_details>pre-edge</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="bb" wavelength="1.3857">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>17.20</VRPTx:f_double_prime>
<VRPTx:f_prime>-31.22</VRPTx:f_prime>
<VRPTx:wavelength_details>peak</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="cc" wavelength="1.3852">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>29.17</VRPTx:f_double_prime>
<VRPTx:f_prime>-13.97</VRPTx:f_prime>
<VRPTx:wavelength_details>edge</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="dd" wavelength="1.3847">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>17.34</VRPTx:f_double_prime>
<VRPTx:f_prime>-6.67</VRPTx:f_prime>
<VRPTx:wavelength_details>remote</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="ee" wavelength="1.3857">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>14.84</VRPTx:f_double_prime>
<VRPTx:f_prime>-28.33</VRPTx:f_prime>
<VRPTx:wavelength_details>ascending edge</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="ff" wavelength="1.3852">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>30.23</VRPTx:f_double_prime>
<VRPTx:f_prime>-21.50</VRPTx:f_prime>
<VRPTx:wavelength_details>peak</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="gg" wavelength="1.3847">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>20.35</VRPTx:f_double_prime>
<VRPTx:f_prime>-10.71</VRPTx:f_prime>
<VRPTx:wavelength_details>descending edge</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="hh" wavelength="1.3784">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>11.84</VRPTx:f_double_prime>
<VRPTx:f_prime>-14.45</VRPTx:f_prime>
<VRPTx:wavelength_details>remote 1</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="ii" wavelength="1.2862">
<VRPTx:d_res_high>3.00</VRPTx:d_res_high>
<VRPTx:d_res_low>20.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>9.01</VRPTx:f_double_prime>
<VRPTx:f_prime>-9.03</VRPTx:f_prime>
<VRPTx:wavelength_details>remote 2</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="jj" wavelength="0.7263">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>4.08</VRPTx:f_double_prime>
<VRPTx:f_prime>-21.10</VRPTx:f_prime>
<VRPTx:wavelength_details>pre-edge</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="kk" wavelength="0.7251">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>7.92</VRPTx:f_double_prime>
<VRPTx:f_prime>-34.72</VRPTx:f_prime>
<VRPTx:wavelength_details>edge</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="ll" wavelength="0.7248">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>10.30</VRPTx:f_double_prime>
<VRPTx:f_prime>-24.87</VRPTx:f_prime>
<VRPTx:wavelength_details>peak</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="mm" wavelength="0.7246">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>9.62</VRPTx:f_double_prime>
<VRPTx:f_prime>-17.43</VRPTx:f_prime>
<VRPTx:wavelength_details>descending edge</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
<VRPTx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="nn" wavelength="0.7217">
<VRPTx:d_res_high>1.90</VRPTx:d_res_high>
<VRPTx:d_res_low>15.00</VRPTx:d_res_low>
<VRPTx:f_double_prime>8.40</VRPTx:f_double_prime>
<VRPTx:f_prime>-13.26</VRPTx:f_prime>
<VRPTx:wavelength_details>remote</VRPTx:wavelength_details>
</VRPTx:phasing_MAD_set>
</VRPTx:phasing_MAD_setCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_MAD_set.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_MIRType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_MIR category record details about
the phasing of the structure where methods involving isomorphous
replacement are involved.
All isomorphous-replacement-based techniques are covered
by this category, including single isomorphous replacement (SIR),
multiple isomorphous replacement (MIR) and single or multiple
isomorphous replacement plus anomalous scattering (SIRAS, MIRAS).
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738].
<VRPTx:phasing_MIRCategory>
<VRPTx:phasing_MIR entry_id="1ABC">
<VRPTx:method> Standard phase refinement (Blow & Crick, 1959)</VRPTx:method>
</VRPTx:phasing_MIR>
</VRPTx:phasing_MIRCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_MIR.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_MIR_derType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_MIR_DER category record details
about individual derivatives used in the phasing of the
structure when methods involving isomorphous replacement are
involved.
A derivative in this context does not necessarily equate with
a data set; for instance, the same data set could be used to
one resolution limit as an isomorphous scatterer and to a
different resolution (and with a different sigma cutoff) as an
anomalous scatterer. These would be treated as two distinct
derivatives, although both derivatives would point to the same
data sets via attribute der_set_id in category phasing_MIR_der and
attribute native_set_id in category phasing_MIR_der.
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738].
<VRPTx:phasing_MIR_derCategory>
<VRPTx:phasing_MIR_der id="KAu(CN)2">
<VRPTx:details>major site interpreted in difference Patterson</VRPTx:details>
<VRPTx:number_of_sites>3</VRPTx:number_of_sites>
</VRPTx:phasing_MIR_der>
<VRPTx:phasing_MIR_der id="K2HgI4">
<VRPTx:details>sites found in cross-difference Fourier</VRPTx:details>
<VRPTx:number_of_sites>6</VRPTx:number_of_sites>
</VRPTx:phasing_MIR_der>
<VRPTx:phasing_MIR_der id="K3IrCl6">
<VRPTx:details>sites found in cross-difference Fourier</VRPTx:details>
<VRPTx:number_of_sites>2</VRPTx:number_of_sites>
</VRPTx:phasing_MIR_der>
<VRPTx:phasing_MIR_der id="All">
<VRPTx:details>data for all three derivatives combined</VRPTx:details>
<VRPTx:number_of_sites>11</VRPTx:number_of_sites>
</VRPTx:phasing_MIR_der>
</VRPTx:phasing_MIR_derCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_MIR_der.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_MIR_der_reflnType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_MIR_DER_REFLN category record details
about the calculated structure factors obtained in an MIR
phasing experiment.
This list may contain information from a number of different
derivatives; attribute der_id in category phasing_MIR_der_refln indicates to which
derivative a given record corresponds. (A derivative in this
context does not necessarily equate with a data set; see the
definition of the PHASING_MIR_DER category for a
discussion of the meaning of derivative.)
It is not necessary for the data items describing the measured
value of F to appear in this list, as they will be
given in the PHASING_SET_REFLN category. However, these
items can also be listed here for completeness.
Example 1 - based on laboratory records for the 6,1,25 reflection
of an Hg/Pt derivative of protein NS1.
<VRPTx:phasing_MIR_der_reflnCategory>
<VRPTx:phasing_MIR_der_refln der_id="HGPT1" index_h="6" index_k="1" index_l="25" set_id="NS1-96">
<VRPTx:F_calc_au>106.66</VRPTx:F_calc_au>
<VRPTx:F_meas_au>204.67</VRPTx:F_meas_au>
<VRPTx:F_meas_sigma>6.21</VRPTx:F_meas_sigma>
<VRPTx:HL_A_iso>-3.15</VRPTx:HL_A_iso>
<VRPTx:HL_B_iso>-0.76</VRPTx:HL_B_iso>
<VRPTx:HL_C_iso>0.65</VRPTx:HL_C_iso>
<VRPTx:HL_D_iso>0.23</VRPTx:HL_D_iso>
<VRPTx:phase_calc>194.48</VRPTx:phase_calc>
</VRPTx:phasing_MIR_der_refln>
</VRPTx:phasing_MIR_der_reflnCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_MIR_der_refln.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_MIR_der_shellType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_MIR_DER_SHELL category record
statistics, broken down into shells of resolution, for an MIR
phasing experiment.
This list may contain information from a number of different
derivatives; attribute der_id in category phasing_MIR_der_shell indicates to which
derivative a given record corresponds. (A derivative in this
context does not necessarily equate with a data set; see the
definition of the PHASING_MIR_DER category for a
discussion of the meaning of derivative.)
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738]
with addition of an arbitrary low-resolution limit.
<VRPTx:phasing_MIR_der_shellCategory>
<VRPTx:phasing_MIR_der_shell d_res_high="8.3" d_res_low="15.0" der_id="KAu(CN)2">
<VRPTx:ha_ampl>54</VRPTx:ha_ampl>
<VRPTx:loc>26</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="6.4" d_res_low="8.3" der_id="KAu(CN)2">
<VRPTx:ha_ampl>54</VRPTx:ha_ampl>
<VRPTx:loc>20</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="5.2" d_res_low="6.4" der_id="KAu(CN)2">
<VRPTx:ha_ampl>50</VRPTx:ha_ampl>
<VRPTx:loc>20</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="4.4" d_res_low="5.2" der_id="KAu(CN)2">
<VRPTx:ha_ampl>44</VRPTx:ha_ampl>
<VRPTx:loc>23</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="3.8" d_res_low="4.4" der_id="KAu(CN)2">
<VRPTx:ha_ampl>39</VRPTx:ha_ampl>
<VRPTx:loc>23</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="3.4" d_res_low="3.8" der_id="KAu(CN)2">
<VRPTx:ha_ampl>33</VRPTx:ha_ampl>
<VRPTx:loc>21</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="3.4" der_id="KAu(CN)2">
<VRPTx:ha_ampl>28</VRPTx:ha_ampl>
<VRPTx:loc>17</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="15.0" der_id="KAu(CN)2">
<VRPTx:ha_ampl>38</VRPTx:ha_ampl>
<VRPTx:loc>21</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="8.3" d_res_low="15.0" der_id="K2HgI4">
<VRPTx:ha_ampl>149</VRPTx:ha_ampl>
<VRPTx:loc>87</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="6.4" d_res_low="8.3" der_id="K2HgI4">
<VRPTx:ha_ampl>121</VRPTx:ha_ampl>
<VRPTx:loc>73</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="5.2" d_res_low="6.4" der_id="K2HgI4">
<VRPTx:ha_ampl>95</VRPTx:ha_ampl>
<VRPTx:loc>61</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="4.4" d_res_low="5.2" der_id="K2HgI4">
<VRPTx:ha_ampl>80</VRPTx:ha_ampl>
<VRPTx:loc>60</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="3.8" d_res_low="4.4" der_id="K2HgI4">
<VRPTx:ha_ampl>73</VRPTx:ha_ampl>
<VRPTx:loc>63</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="3.4" d_res_low="3.8" der_id="K2HgI4">
<VRPTx:ha_ampl>68</VRPTx:ha_ampl>
<VRPTx:loc>57</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="3.4" der_id="K2HgI4">
<VRPTx:ha_ampl>63</VRPTx:ha_ampl>
<VRPTx:loc>46</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="15.0" der_id="K2HgI4">
<VRPTx:ha_ampl>79</VRPTx:ha_ampl>
<VRPTx:loc>58</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="8.3" d_res_low="15.0" der_id="K3IrCl6">
<VRPTx:ha_ampl>33</VRPTx:ha_ampl>
<VRPTx:loc>27</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="6.4" d_res_low="8.3" der_id="K3IrCl6">
<VRPTx:ha_ampl>40</VRPTx:ha_ampl>
<VRPTx:loc>23</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="5.2" d_res_low="6.4" der_id="K3IrCl6">
<VRPTx:ha_ampl>31</VRPTx:ha_ampl>
<VRPTx:loc>22</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="4.4" d_res_low="5.2" der_id="K3IrCl6">
<VRPTx:ha_ampl>27</VRPTx:ha_ampl>
<VRPTx:loc>23</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="3.8" d_res_low="4.4" der_id="K3IrCl6">
<VRPTx:ha_ampl>22</VRPTx:ha_ampl>
<VRPTx:loc>23</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="3.4" d_res_low="3.8" der_id="K3IrCl6">
<VRPTx:ha_ampl>19</VRPTx:ha_ampl>
<VRPTx:loc>20</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="3.4" der_id="K3IrCl6">
<VRPTx:ha_ampl>16</VRPTx:ha_ampl>
<VRPTx:loc>20</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
<VRPTx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="15.0" der_id="K3IrCl6">
<VRPTx:ha_ampl>23</VRPTx:ha_ampl>
<VRPTx:loc>21</VRPTx:loc>
</VRPTx:phasing_MIR_der_shell>
</VRPTx:phasing_MIR_der_shellCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_MIR_der_shell.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_MIR_der_siteType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_MIR_DER_SITE category record details
about the heavy-atom sites in an MIR phasing experiment.
This list may contain information from a number of different
derivatives; attribute der_id in category phasing_MIR_der_site indicates to which
derivative a given record corresponds. (A derivative in this
context does not necessarily equate with a data set; see the
definition of the PHASING_MIR_DER category for a
discussion of the meaning of derivative.)
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738]
with occupancies converted from electrons to fractional.
<VRPTx:phasing_MIR_der_siteCategory>
<VRPTx:phasing_MIR_der_site der_id="KAu(CN)2" id="1">
<VRPTx:B_iso>33.0</VRPTx:B_iso>
<VRPTx:atom_type_symbol>Au</VRPTx:atom_type_symbol>
<VRPTx:fract_x>0.082</VRPTx:fract_x>
<VRPTx:fract_y>0.266</VRPTx:fract_y>
<VRPTx:fract_z>0.615</VRPTx:fract_z>
<VRPTx:occupancy>0.40</VRPTx:occupancy>
</VRPTx:phasing_MIR_der_site>
<VRPTx:phasing_MIR_der_site der_id="KAu(CN)2" id="2">
<VRPTx:B_iso>25.9</VRPTx:B_iso>
<VRPTx:atom_type_symbol>Au</VRPTx:atom_type_symbol>
<VRPTx:fract_x>0.607</VRPTx:fract_x>
<VRPTx:fract_y>0.217</VRPTx:fract_y>
<VRPTx:fract_z>0.816</VRPTx:fract_z>
<VRPTx:occupancy>0.03</VRPTx:occupancy>
</VRPTx:phasing_MIR_der_site>
<VRPTx:phasing_MIR_der_site der_id="KAu(CN)2" id="3">
<VRPTx:B_iso>15.7</VRPTx:B_iso>
<VRPTx:atom_type_symbol>Au</VRPTx:atom_type_symbol>
<VRPTx:fract_x>0.263</VRPTx:fract_x>
<VRPTx:fract_y>0.782</VRPTx:fract_y>
<VRPTx:fract_z>0.906</VRPTx:fract_z>
<VRPTx:occupancy>0.02</VRPTx:occupancy>
</VRPTx:phasing_MIR_der_site>
<VRPTx:phasing_MIR_der_site der_id="K2HgI4" id="1">
<VRPTx:B_iso>33.7</VRPTx:B_iso>
<VRPTx:atom_type_symbol>Hg</VRPTx:atom_type_symbol>
<VRPTx:fract_x>0.048</VRPTx:fract_x>
<VRPTx:fract_y>0.286</VRPTx:fract_y>
<VRPTx:fract_z>0.636</VRPTx:fract_z>
<VRPTx:occupancy>0.63</VRPTx:occupancy>
</VRPTx:phasing_MIR_der_site>
<VRPTx:phasing_MIR_der_site der_id="K2HgI4" id="2">
<VRPTx:B_iso>36.7</VRPTx:B_iso>
<VRPTx:atom_type_symbol>Hg</VRPTx:atom_type_symbol>
<VRPTx:fract_x>0.913</VRPTx:fract_x>
<VRPTx:fract_y>0.768</VRPTx:fract_y>
<VRPTx:fract_z>0.889</VRPTx:fract_z>
<VRPTx:occupancy>0.34</VRPTx:occupancy>
</VRPTx:phasing_MIR_der_site>
<VRPTx:phasing_MIR_der_site der_id="K2HgI4" id="3">
<VRPTx:B_iso>24.2</VRPTx:B_iso>
<VRPTx:atom_type_symbol>Hg</VRPTx:atom_type_symbol>
<VRPTx:fract_x>0.974</VRPTx:fract_x>
<VRPTx:fract_y>0.455</VRPTx:fract_y>
<VRPTx:fract_z>0.974</VRPTx:fract_z>
<VRPTx:occupancy>0.23</VRPTx:occupancy>
</VRPTx:phasing_MIR_der_site>
<VRPTx:phasing_MIR_der_site der_id="K2HgI4" id="4">
<VRPTx:B_iso>14.7</VRPTx:B_iso>
<VRPTx:atom_type_symbol>Hg</VRPTx:atom_type_symbol>
<VRPTx:fract_x>0.903</VRPTx:fract_x>
<VRPTx:fract_y>0.836</VRPTx:fract_y>
<VRPTx:fract_z>0.859</VRPTx:fract_z>
<VRPTx:occupancy>0.28</VRPTx:occupancy>
</VRPTx:phasing_MIR_der_site>
<VRPTx:phasing_MIR_der_site der_id="K2HgI4" id="5">
<VRPTx:B_iso>6.4</VRPTx:B_iso>
<VRPTx:atom_type_symbol>Hg</VRPTx:atom_type_symbol>
<VRPTx:fract_x>0.489</VRPTx:fract_x>
<VRPTx:fract_y>0.200</VRPTx:fract_y>
<VRPTx:fract_z>0.885</VRPTx:fract_z>
<VRPTx:occupancy>0.07</VRPTx:occupancy>
</VRPTx:phasing_MIR_der_site>
<VRPTx:phasing_MIR_der_site der_id="K2HgI4" id="6">
<VRPTx:B_iso>32.9</VRPTx:B_iso>
<VRPTx:atom_type_symbol>Hg</VRPTx:atom_type_symbol>
<VRPTx:fract_x>0.162</VRPTx:fract_x>
<VRPTx:fract_y>0.799</VRPTx:fract_y>
<VRPTx:fract_z>0.889</VRPTx:fract_z>
<VRPTx:occupancy>0.07</VRPTx:occupancy>
</VRPTx:phasing_MIR_der_site>
<VRPTx:phasing_MIR_der_site der_id="K3IrCl6" id="1">
<VRPTx:B_iso>40.8</VRPTx:B_iso>
<VRPTx:atom_type_symbol>Ir</VRPTx:atom_type_symbol>
<VRPTx:fract_x>0.209</VRPTx:fract_x>
<VRPTx:fract_y>0.739</VRPTx:fract_y>
<VRPTx:fract_z>0.758</VRPTx:fract_z>
<VRPTx:occupancy>0.26</VRPTx:occupancy>
</VRPTx:phasing_MIR_der_site>
<VRPTx:phasing_MIR_der_site der_id="K3IrCl6" id="2">
<VRPTx:B_iso>24.9</VRPTx:B_iso>
<VRPTx:atom_type_symbol>Ir</VRPTx:atom_type_symbol>
<VRPTx:fract_x>0.279</VRPTx:fract_x>
<VRPTx:fract_y>0.613</VRPTx:fract_y>
<VRPTx:fract_z>0.752</VRPTx:fract_z>
<VRPTx:occupancy>0.05</VRPTx:occupancy>
</VRPTx:phasing_MIR_der_site>
</VRPTx:phasing_MIR_der_siteCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_MIR_der_site.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_MIR_shellType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_MIR_SHELL category record statistics
for an isomorphous replacement phasing experiment.broken
down into shells of resolution.
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738]
with addition of an arbitrary low-resolution limit.
<VRPTx:phasing_MIR_shellCategory>
<VRPTx:phasing_MIR_shell d_res_high="8.3" d_res_low="15.0">
<VRPTx:FOM>0.69</VRPTx:FOM>
<VRPTx:reflns>80</VRPTx:reflns>
</VRPTx:phasing_MIR_shell>
<VRPTx:phasing_MIR_shell d_res_high="6.4" d_res_low="8.3">
<VRPTx:FOM>0.73</VRPTx:FOM>
<VRPTx:reflns>184</VRPTx:reflns>
</VRPTx:phasing_MIR_shell>
<VRPTx:phasing_MIR_shell d_res_high="5.2" d_res_low="6.4">
<VRPTx:FOM>0.72</VRPTx:FOM>
<VRPTx:reflns>288</VRPTx:reflns>
</VRPTx:phasing_MIR_shell>
<VRPTx:phasing_MIR_shell d_res_high="4.4" d_res_low="5.2">
<VRPTx:FOM>0.65</VRPTx:FOM>
<VRPTx:reflns>406</VRPTx:reflns>
</VRPTx:phasing_MIR_shell>
<VRPTx:phasing_MIR_shell d_res_high="3.8" d_res_low="4.4">
<VRPTx:FOM>0.54</VRPTx:FOM>
<VRPTx:reflns>554</VRPTx:reflns>
</VRPTx:phasing_MIR_shell>
<VRPTx:phasing_MIR_shell d_res_high="3.4" d_res_low="3.8">
<VRPTx:FOM>0.53</VRPTx:FOM>
<VRPTx:reflns>730</VRPTx:reflns>
</VRPTx:phasing_MIR_shell>
<VRPTx:phasing_MIR_shell d_res_high="3.0" d_res_low="3.4">
<VRPTx:FOM>0.50</VRPTx:FOM>
<VRPTx:reflns>939</VRPTx:reflns>
</VRPTx:phasing_MIR_shell>
</VRPTx:phasing_MIR_shellCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_MIR_shell.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_averagingType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_AVERAGING category record details
about the phasing of the structure where methods involving
averaging of multiple observations of the molecule in the
asymmetric unit are involved.
Example 1 - hypothetical example.
<VRPTx:phasing_averagingCategory>
<VRPTx:phasing_averaging entry_id="EXAMHYPO">
<VRPTx:details> The position of the threefold axis was redetermined every
five cycles.</VRPTx:details>
<VRPTx:method> Iterative threefold averaging alternating with phase
extensions by 0.5 reciprocal lattice units per cycle.</VRPTx:method>
</VRPTx:phasing_averaging>
</VRPTx:phasing_averagingCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_averaging.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_isomorphousType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_ISOMORPHOUS category record details
about the phasing of the structure where a model isomorphous
to the structure being phased was used to generate the initial
phases.
Example 1 - based on PDB entry 4PHV and laboratory records for the
structure corresponding to PDB entry 4PHV.
<VRPTx:phasing_isomorphousCategory>
<VRPTx:phasing_isomorphous entry_id="1ABC">
<VRPTx:details> The inhibitor and all solvent atoms were removed from the
parent structure before beginning refinement. All static
disorder present in the parent structure was also removed.</VRPTx:details>
<VRPTx:parent>PDB entry 5HVP</VRPTx:parent>
</VRPTx:phasing_isomorphous>
</VRPTx:phasing_isomorphousCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_isomorphous.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_setType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_SET category record details about
the data sets used in a phasing experiment. A given data set
may be used in a number of different ways; for instance, a
single data set could be used both as an isomorphous derivative
and as a component of a multiple-wavelength calculation. This
category establishes identifiers for each data set and permits
the archiving of a subset of experimental information for each
data set (cell constants, wavelength, temperature etc.).
This and related categories of data items are provided so that
derivative intensity and phase information can be stored in
the same data block as the information for the refined
structure.
If all the possible experimental information for each data
set (raw data sets, crystal growth conditions etc.) is to be
archived, these data items should be recorded in a separate
data block.
Example 1 - based on laboratory records for an Hg/Pt derivative of
protein NS1.
<VRPTx:phasing_setCategory>
<VRPTx:phasing_set id="NS1-96">
<VRPTx:cell_angle_alpha>90.0</VRPTx:cell_angle_alpha>
<VRPTx:cell_angle_beta>90.0</VRPTx:cell_angle_beta>
<VRPTx:cell_angle_gamma>90.0</VRPTx:cell_angle_gamma>
<VRPTx:cell_length_a>38.63</VRPTx:cell_length_a>
<VRPTx:cell_length_b>38.63</VRPTx:cell_length_b>
<VRPTx:cell_length_c>82.88</VRPTx:cell_length_c>
<VRPTx:detector_specific>RXII</VRPTx:detector_specific>
<VRPTx:detector_type>image plate</VRPTx:detector_type>
<VRPTx:radiation_wavelength>1.5145</VRPTx:radiation_wavelength>
</VRPTx:phasing_set>
</VRPTx:phasing_setCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_set.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | phasing_set_reflnType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the PHASING_SET_REFLN category record the values
of the measured structure factors used in a phasing experiment.
This list may contain information from a number of different
data sets; attribute set_id in category phasing_set_refln indicates the data set
to which a given record corresponds.
Example 1 - based on laboratory records for the 15,15,32
reflection of an Hg/Pt derivative of protein NS1.
<VRPTx:phasing_set_reflnCategory>
<VRPTx:phasing_set_refln index_h="15" index_k="15" index_l="32" set_id="NS1-96">
<VRPTx:F_meas_au>181.79</VRPTx:F_meas_au>
<VRPTx:F_meas_sigma_au>3.72</VRPTx:F_meas_sigma_au>
</VRPTx:phasing_set_refln>
</VRPTx:phasing_set_reflnCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/phasing_set_refln.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | refineType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFINE category record details about the
structure-refinement parameters.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:refineCategory>
<VRPTx:refine entry_id="5HVP" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:ls_R_factor_obs>0.176</VRPTx:ls_R_factor_obs>
<VRPTx:ls_number_parameters>7032</VRPTx:ls_number_parameters>
<VRPTx:ls_number_reflns_obs>12901</VRPTx:ls_number_reflns_obs>
<VRPTx:ls_number_restraints>6609</VRPTx:ls_number_restraints>
<VRPTx:ls_weighting_details> Sigdel model of Konnert-Hendrickson:
Sigdel: Afsig + Bfsig*(sin(theta)/lambda-1/6)
Afsig = 22.0, Bfsig = -150.0 at beginning of refinement
Afsig = 15.5, Bfsig = -50.0 at end of refinement</VRPTx:ls_weighting_details>
<VRPTx:ls_weighting_scheme>calc</VRPTx:ls_weighting_scheme>
</VRPTx:refine>
</VRPTx:refineCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<VRPTx:refineCategory>
<VRPTx:refine entry_id="TOZ" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:details>sfls:_F_calc_weight_full_matrix</VRPTx:details>
<VRPTx:diff_density_max>.131</VRPTx:diff_density_max>
<VRPTx:diff_density_min>-.108</VRPTx:diff_density_min>
<VRPTx:ls_R_factor_all>.038</VRPTx:ls_R_factor_all>
<VRPTx:ls_R_factor_obs>.034</VRPTx:ls_R_factor_obs>
<VRPTx:ls_abs_structure_Flack>0</VRPTx:ls_abs_structure_Flack>
<VRPTx:ls_abs_structure_details> The absolute configuration was assigned to agree with the
known chirality at C3 arising from its precursor l-leucine.</VRPTx:ls_abs_structure_details>
<VRPTx:ls_extinction_coef>3514</VRPTx:ls_extinction_coef>
<VRPTx:ls_extinction_expression> Larson, A. C. (1970). "Crystallographic Computing", edited
by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard.</VRPTx:ls_extinction_expression>
<VRPTx:ls_extinction_method>Zachariasen</VRPTx:ls_extinction_method>
<VRPTx:ls_goodness_of_fit_all>1.462</VRPTx:ls_goodness_of_fit_all>
<VRPTx:ls_goodness_of_fit_obs>1.515</VRPTx:ls_goodness_of_fit_obs>
<VRPTx:ls_hydrogen_treatment>refxyz except H332B noref</VRPTx:ls_hydrogen_treatment>
<VRPTx:ls_matrix_type>full</VRPTx:ls_matrix_type>
<VRPTx:ls_number_constraints>0</VRPTx:ls_number_constraints>
<VRPTx:ls_number_parameters>272</VRPTx:ls_number_parameters>
<VRPTx:ls_number_reflns_obs>1408</VRPTx:ls_number_reflns_obs>
<VRPTx:ls_number_restraints>0</VRPTx:ls_number_restraints>
<VRPTx:ls_shift_over_esd_max>.535</VRPTx:ls_shift_over_esd_max>
<VRPTx:ls_shift_over_esd_mean>.044</VRPTx:ls_shift_over_esd_mean>
<VRPTx:ls_structure_factor_coef>F</VRPTx:ls_structure_factor_coef>
<VRPTx:ls_wR_factor_all>.044</VRPTx:ls_wR_factor_all>
<VRPTx:ls_wR_factor_obs>.042</VRPTx:ls_wR_factor_obs>
<VRPTx:ls_weighting_details>w=1/(\s^2^(F)+0.0004F^2^)</VRPTx:ls_weighting_details>
<VRPTx:ls_weighting_scheme>calc</VRPTx:ls_weighting_scheme>
</VRPTx:refine>
</VRPTx:refineCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refine.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | refine_B_isoType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFINE_B_ISO category record details about
the treatment of isotropic B factors (displacement parameters)
during refinement.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:refine_B_isoCategory>
<VRPTx:refine_B_iso class="protein" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:treatment>isotropic</VRPTx:treatment>
</VRPTx:refine_B_iso>
<VRPTx:refine_B_iso class="solvent" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:treatment>isotropic</VRPTx:treatment>
</VRPTx:refine_B_iso>
<VRPTx:refine_B_iso class="inhibitor" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:treatment>isotropic</VRPTx:treatment>
</VRPTx:refine_B_iso>
</VRPTx:refine_B_isoCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refine_B_iso.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | refine_analyzeType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFINE_ANALYZE category record details
about the refined structure that are often used to analyze the
refinement and assess its quality. A given computer program
may or may not produce values corresponding to these data
names.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:refine_analyzeCategory>
<VRPTx:refine_analyze entry_id="5HVP" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:Luzzati_coordinate_error_obs>0.056</VRPTx:Luzzati_coordinate_error_obs>
<VRPTx:Luzzati_d_res_low_obs>2.51</VRPTx:Luzzati_d_res_low_obs>
</VRPTx:refine_analyze>
</VRPTx:refine_analyzeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refine_analyze.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | refine_funct_minimizedType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFINE_FUNCT_MINIMIZED category record
details about the individual terms of the function minimized
during refinement.
Example 1 - based on RESTRAIN refinement for the CCP4 test data set
toxd.
<VRPTx:refine_funct_minimizedCategory>
<VRPTx:refine_funct_minimized pdbx_refine_id="X-RAY DIFFRACTION" type="sum(W*Delta(Amplitude)^2">
<VRPTx:number_terms>3009</VRPTx:number_terms>
<VRPTx:residual>1621.3</VRPTx:residual>
</VRPTx:refine_funct_minimized>
<VRPTx:refine_funct_minimized pdbx_refine_id="X-RAY DIFFRACTION" type="sum(W*Delta(Plane+Rigid)^2">
<VRPTx:number_terms>85</VRPTx:number_terms>
<VRPTx:residual>56.68</VRPTx:residual>
</VRPTx:refine_funct_minimized>
<VRPTx:refine_funct_minimized pdbx_refine_id="X-RAY DIFFRACTION" type="sum(W*Delta(Distance)^2">
<VRPTx:number_terms>1219</VRPTx:number_terms>
<VRPTx:residual>163.59</VRPTx:residual>
</VRPTx:refine_funct_minimized>
<VRPTx:refine_funct_minimized pdbx_refine_id="X-RAY DIFFRACTION" type="sum(W*Delta(U-tempfactors)^2">
<VRPTx:number_terms>1192</VRPTx:number_terms>
<VRPTx:residual>69.338</VRPTx:residual>
</VRPTx:refine_funct_minimized>
</VRPTx:refine_funct_minimizedCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refine_funct_minimized.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | refine_histType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFINE_HIST category record details about the
steps during the refinement of the structure.
These data items are not meant to be as thorough a description
of the refinement as is provided for the final model in other
categories; rather, these data items provide a mechanism for
sketching out the progress of the refinement, supported by a
small set of representative statistics.
Example 1 - based on laboratory records for the collagen-like
peptide [(POG)4 EKG (POG)5]3.
<VRPTx:refine_histCategory>
<VRPTx:refine_hist cycle_id="C134" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:R_factor_R_free>.274</VRPTx:R_factor_R_free>
<VRPTx:R_factor_R_work>.160</VRPTx:R_factor_R_work>
<VRPTx:R_factor_all>.265</VRPTx:R_factor_all>
<VRPTx:R_factor_obs>.195</VRPTx:R_factor_obs>
<VRPTx:d_res_high>1.85</VRPTx:d_res_high>
<VRPTx:d_res_low>20.0</VRPTx:d_res_low>
<VRPTx:details> Add majority of solvent molecules. B factors refined by
group. Continued to remove misplaced water molecules.</VRPTx:details>
<VRPTx:number_atoms_solvent>217</VRPTx:number_atoms_solvent>
<VRPTx:number_atoms_total>808</VRPTx:number_atoms_total>
<VRPTx:number_reflns_R_free>476</VRPTx:number_reflns_R_free>
<VRPTx:number_reflns_R_work>4410</VRPTx:number_reflns_R_work>
<VRPTx:number_reflns_all>6174</VRPTx:number_reflns_all>
<VRPTx:number_reflns_obs>4886</VRPTx:number_reflns_obs>
</VRPTx:refine_hist>
</VRPTx:refine_histCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refine_hist.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | refine_ls_classType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFINE_LS_CLASS category record details
about the reflections used for the structure refinement
for each reflection class separately.
Example 1 - data for a modulated structure from van Smaalen
[J. Phys. Condens. Matter (1991), 3, 1247-1263].
<VRPTx:refine_ls_classCategory>
<VRPTx:refine_ls_class code="Main">
<VRPTx:R_factor_gt>0.057</VRPTx:R_factor_gt>
</VRPTx:refine_ls_class>
<VRPTx:refine_ls_class code="Com">
<VRPTx:R_factor_gt>0.074</VRPTx:R_factor_gt>
</VRPTx:refine_ls_class>
<VRPTx:refine_ls_class code="NbRefls">
<VRPTx:R_factor_gt>0.064</VRPTx:R_factor_gt>
</VRPTx:refine_ls_class>
<VRPTx:refine_ls_class code="LaRefls">
<VRPTx:R_factor_gt>0.046</VRPTx:R_factor_gt>
</VRPTx:refine_ls_class>
<VRPTx:refine_ls_class code="Sat1">
<VRPTx:R_factor_gt>0.112</VRPTx:R_factor_gt>
</VRPTx:refine_ls_class>
<VRPTx:refine_ls_class code="Sat2">
<VRPTx:R_factor_gt>0.177</VRPTx:R_factor_gt>
</VRPTx:refine_ls_class>
</VRPTx:refine_ls_classCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refine_ls_class.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | refine_ls_restrType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFINE_LS_RESTR category record details about
the restraints applied to various classes of parameters during
the least-squares refinement.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:refine_ls_restrCategory>
<VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="bond_d">
<VRPTx:criterion>> 2\s</VRPTx:criterion>
<VRPTx:dev_ideal>0.018</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.020</VRPTx:dev_ideal_target>
<VRPTx:number>1654</VRPTx:number>
<VRPTx:rejects>22</VRPTx:rejects>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="angle_d">
<VRPTx:criterion>> 2\s</VRPTx:criterion>
<VRPTx:dev_ideal>0.038</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.030</VRPTx:dev_ideal_target>
<VRPTx:number>2246</VRPTx:number>
<VRPTx:rejects>139</VRPTx:rejects>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="planar_d">
<VRPTx:criterion>> 2\s</VRPTx:criterion>
<VRPTx:dev_ideal>0.043</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.040</VRPTx:dev_ideal_target>
<VRPTx:number>498</VRPTx:number>
<VRPTx:rejects>21</VRPTx:rejects>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="planar">
<VRPTx:criterion>> 2\s</VRPTx:criterion>
<VRPTx:dev_ideal>0.015</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.020</VRPTx:dev_ideal_target>
<VRPTx:number>270</VRPTx:number>
<VRPTx:rejects>1</VRPTx:rejects>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="chiral">
<VRPTx:criterion>> 2\s</VRPTx:criterion>
<VRPTx:dev_ideal>0.177</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.150</VRPTx:dev_ideal_target>
<VRPTx:number>278</VRPTx:number>
<VRPTx:rejects>2</VRPTx:rejects>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="singtor_nbd">
<VRPTx:criterion>> 2\s</VRPTx:criterion>
<VRPTx:dev_ideal>0.216</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.500</VRPTx:dev_ideal_target>
<VRPTx:number>582</VRPTx:number>
<VRPTx:rejects>0</VRPTx:rejects>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="multtor_nbd">
<VRPTx:criterion>> 2\s</VRPTx:criterion>
<VRPTx:dev_ideal>0.207</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.500</VRPTx:dev_ideal_target>
<VRPTx:number>419</VRPTx:number>
<VRPTx:rejects>0</VRPTx:rejects>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="xyhbond_nbd">
<VRPTx:criterion>> 2\s</VRPTx:criterion>
<VRPTx:dev_ideal>0.245</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.500</VRPTx:dev_ideal_target>
<VRPTx:number>149</VRPTx:number>
<VRPTx:rejects>0</VRPTx:rejects>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="planar_tor">
<VRPTx:criterion>> 2\s</VRPTx:criterion>
<VRPTx:dev_ideal>2.6</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>3.0</VRPTx:dev_ideal_target>
<VRPTx:number>203</VRPTx:number>
<VRPTx:rejects>9</VRPTx:rejects>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="staggered_tor">
<VRPTx:criterion>> 2\s</VRPTx:criterion>
<VRPTx:dev_ideal>17.4</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>15.0</VRPTx:dev_ideal_target>
<VRPTx:number>298</VRPTx:number>
<VRPTx:rejects>31</VRPTx:rejects>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="orthonormal_tor">
<VRPTx:criterion>> 2\s</VRPTx:criterion>
<VRPTx:dev_ideal>18.1</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>20.0</VRPTx:dev_ideal_target>
<VRPTx:number>12</VRPTx:number>
<VRPTx:rejects>1</VRPTx:rejects>
</VRPTx:refine_ls_restr>
</VRPTx:refine_ls_restrCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refine_ls_restr.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | refine_ls_restr_ncsType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFINE_LS_RESTR_NCS category record details
about the restraints applied to atom positions in domains
related by noncrystallographic symmetry during least-squares
refinement, and also about the deviation of the restrained
atomic parameters at the end of the refinement. It is
expected that these values will only be reported once for each
set of restrained domains.
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
<VRPTx:refine_ls_restr_ncsCategory>
<VRPTx:refine_ls_restr_ncs pdbx_ordinal="1">
<VRPTx:dom_id>d2</VRPTx:dom_id>
<VRPTx:ncs_model_details>
NCS restraint for pseudo-twofold symmetry between domains
d1 and d2. Position weight coefficient given in
Kcal/(mol \%A^2^) and isotropic B weight coefficient given
in \%A^2^.</VRPTx:ncs_model_details>
<VRPTx:pdbx_asym_id>A</VRPTx:pdbx_asym_id>
<VRPTx:pdbx_ens_id>1</VRPTx:pdbx_ens_id>
<VRPTx:pdbx_refine_id>X-RAY DIFFRACTION</VRPTx:pdbx_refine_id>
<VRPTx:pdbx_type>medium positional</VRPTx:pdbx_type>
<VRPTx:rms_dev_B_iso>0.16</VRPTx:rms_dev_B_iso>
<VRPTx:rms_dev_position>0.09</VRPTx:rms_dev_position>
<VRPTx:weight_B_iso>2.0</VRPTx:weight_B_iso>
<VRPTx:weight_position>300.0</VRPTx:weight_position>
</VRPTx:refine_ls_restr_ncs>
</VRPTx:refine_ls_restr_ncsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refine_ls_restr_ncs.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | refine_ls_restr_typeType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFINE_LS_RESTR_TYPE category record details
about the restraint types used in the least-squares refinement.
Example 1 - based on RESTRAIN refinement for the CCP4 test data set
toxd.
<VRPTx:refine_ls_restrCategory>
<VRPTx:refine_ls_restr type="RESTRAIN_Distances < 2.12">
<VRPTx:dev_ideal>0.005</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.022</VRPTx:dev_ideal_target>
<VRPTx:number>509</VRPTx:number>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr type="RESTRAIN_Distances 2.12 < D < 2.625">
<VRPTx:dev_ideal>0.016</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.037</VRPTx:dev_ideal_target>
<VRPTx:number>671</VRPTx:number>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr type="RESTRAIN_Distances > 2.625">
<VRPTx:dev_ideal>0.034</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.043</VRPTx:dev_ideal_target>
<VRPTx:number>39</VRPTx:number>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr type="RESTRAIN_Peptide Planes">
<VRPTx:dev_ideal>0.002</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.010</VRPTx:dev_ideal_target>
<VRPTx:number>59</VRPTx:number>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr type="RESTRAIN_Ring and other planes">
<VRPTx:dev_ideal>0.014</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target>0.010</VRPTx:dev_ideal_target>
<VRPTx:number>26</VRPTx:number>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4">
<VRPTx:dev_ideal>0.106</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target xsi:nil="true" />
<VRPTx:number>212</VRPTx:number>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6">
<VRPTx:dev_ideal>0.101</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target xsi:nil="true" />
<VRPTx:number>288</VRPTx:number>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0">
<VRPTx:dev_ideal>0.077</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target xsi:nil="true" />
<VRPTx:number>6</VRPTx:number>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2">
<VRPTx:dev_ideal>0.114</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target xsi:nil="true" />
<VRPTx:number>10</VRPTx:number>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4">
<VRPTx:dev_ideal>0.119</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target xsi:nil="true" />
<VRPTx:number>215</VRPTx:number>
</VRPTx:refine_ls_restr>
<VRPTx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist >2.4">
<VRPTx:dev_ideal>0.106</VRPTx:dev_ideal>
<VRPTx:dev_ideal_target xsi:nil="true" />
<VRPTx:number>461</VRPTx:number>
</VRPTx:refine_ls_restr>
</VRPTx:refine_ls_restrCategory>
<VRPTx:refine_ls_restr_typeCategory>
<VRPTx:refine_ls_restr_type type="RESTRAIN_Distances < 2.12">
<VRPTx:distance_cutoff_high>2.12</VRPTx:distance_cutoff_high>
<VRPTx:distance_cutoff_low xsi:nil="true" />
</VRPTx:refine_ls_restr_type>
<VRPTx:refine_ls_restr_type type="RESTRAIN_Distances 2.12 < D < 2.625">
<VRPTx:distance_cutoff_high>2.625</VRPTx:distance_cutoff_high>
<VRPTx:distance_cutoff_low>2.12</VRPTx:distance_cutoff_low>
</VRPTx:refine_ls_restr_type>
<VRPTx:refine_ls_restr_type type="RESTRAIN_Distances > 2.625">
<VRPTx:distance_cutoff_high xsi:nil="true" />
<VRPTx:distance_cutoff_low>2.625</VRPTx:distance_cutoff_low>
</VRPTx:refine_ls_restr_type>
<VRPTx:refine_ls_restr_type type="RESTRAIN_Peptide Planes">
<VRPTx:distance_cutoff_high xsi:nil="true" />
<VRPTx:distance_cutoff_low xsi:nil="true" />
</VRPTx:refine_ls_restr_type>
<VRPTx:refine_ls_restr_type type="RESTRAIN_Ring and other planes">
<VRPTx:distance_cutoff_high xsi:nil="true" />
<VRPTx:distance_cutoff_low xsi:nil="true" />
</VRPTx:refine_ls_restr_type>
<VRPTx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4">
<VRPTx:distance_cutoff_high>1.4</VRPTx:distance_cutoff_high>
<VRPTx:distance_cutoff_low>1.2</VRPTx:distance_cutoff_low>
</VRPTx:refine_ls_restr_type>
<VRPTx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6">
<VRPTx:distance_cutoff_high>1.6</VRPTx:distance_cutoff_high>
<VRPTx:distance_cutoff_low>1.4</VRPTx:distance_cutoff_low>
</VRPTx:refine_ls_restr_type>
<VRPTx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0">
<VRPTx:distance_cutoff_high>2.0</VRPTx:distance_cutoff_high>
<VRPTx:distance_cutoff_low>1.8</VRPTx:distance_cutoff_low>
</VRPTx:refine_ls_restr_type>
<VRPTx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2">
<VRPTx:distance_cutoff_high>2.2</VRPTx:distance_cutoff_high>
<VRPTx:distance_cutoff_low>2.0</VRPTx:distance_cutoff_low>
</VRPTx:refine_ls_restr_type>
<VRPTx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4">
<VRPTx:distance_cutoff_high>2.4</VRPTx:distance_cutoff_high>
<VRPTx:distance_cutoff_low>2.2</VRPTx:distance_cutoff_low>
</VRPTx:refine_ls_restr_type>
<VRPTx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist >2.4">
<VRPTx:distance_cutoff_high xsi:nil="true" />
<VRPTx:distance_cutoff_low>2.4</VRPTx:distance_cutoff_low>
</VRPTx:refine_ls_restr_type>
</VRPTx:refine_ls_restr_typeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refine_ls_restr_type.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | refine_ls_shellType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFINE_LS_SHELL category record details about
the results of the least-squares refinement broken down into
shells of resolution.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:refine_ls_shellCategory>
<VRPTx:refine_ls_shell d_res_high="4.51" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:R_factor_obs>0.196</VRPTx:R_factor_obs>
<VRPTx:d_res_low>8.00</VRPTx:d_res_low>
<VRPTx:number_reflns_obs>1226</VRPTx:number_reflns_obs>
</VRPTx:refine_ls_shell>
<VRPTx:refine_ls_shell d_res_high="3.48" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:R_factor_obs>0.146</VRPTx:R_factor_obs>
<VRPTx:d_res_low>4.51</VRPTx:d_res_low>
<VRPTx:number_reflns_obs>1679</VRPTx:number_reflns_obs>
</VRPTx:refine_ls_shell>
<VRPTx:refine_ls_shell d_res_high="2.94" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:R_factor_obs>0.160</VRPTx:R_factor_obs>
<VRPTx:d_res_low>3.48</VRPTx:d_res_low>
<VRPTx:number_reflns_obs>2014</VRPTx:number_reflns_obs>
</VRPTx:refine_ls_shell>
<VRPTx:refine_ls_shell d_res_high="2.59" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:R_factor_obs>0.182</VRPTx:R_factor_obs>
<VRPTx:d_res_low>2.94</VRPTx:d_res_low>
<VRPTx:number_reflns_obs>2147</VRPTx:number_reflns_obs>
</VRPTx:refine_ls_shell>
<VRPTx:refine_ls_shell d_res_high="2.34" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:R_factor_obs>0.193</VRPTx:R_factor_obs>
<VRPTx:d_res_low>2.59</VRPTx:d_res_low>
<VRPTx:number_reflns_obs>2127</VRPTx:number_reflns_obs>
</VRPTx:refine_ls_shell>
<VRPTx:refine_ls_shell d_res_high="2.15" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:R_factor_obs>0.203</VRPTx:R_factor_obs>
<VRPTx:d_res_low>2.34</VRPTx:d_res_low>
<VRPTx:number_reflns_obs>2061</VRPTx:number_reflns_obs>
</VRPTx:refine_ls_shell>
<VRPTx:refine_ls_shell d_res_high="2.00" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:R_factor_obs>0.188</VRPTx:R_factor_obs>
<VRPTx:d_res_low>2.15</VRPTx:d_res_low>
<VRPTx:number_reflns_obs>1647</VRPTx:number_reflns_obs>
</VRPTx:refine_ls_shell>
</VRPTx:refine_ls_shellCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refine_ls_shell.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | refine_occupancyType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFINE_OCCUPANCY category record details
about the treatment of atom occupancies during refinement.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:refine_occupancyCategory>
<VRPTx:refine_occupancy class="protein" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:details xsi:nil="true" />
<VRPTx:treatment>fix</VRPTx:treatment>
<VRPTx:value>1.00</VRPTx:value>
</VRPTx:refine_occupancy>
<VRPTx:refine_occupancy class="solvent" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:details xsi:nil="true" />
<VRPTx:treatment>fix</VRPTx:treatment>
<VRPTx:value>1.00</VRPTx:value>
</VRPTx:refine_occupancy>
<VRPTx:refine_occupancy class="inhibitor orientation 1" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:details xsi:nil="true" />
<VRPTx:treatment>fix</VRPTx:treatment>
<VRPTx:value>0.65</VRPTx:value>
</VRPTx:refine_occupancy>
<VRPTx:refine_occupancy class="inhibitor orientation 2" pdbx_refine_id="X-RAY DIFFRACTION">
<VRPTx:details> The inhibitor binds to the enzyme in two alternative
conformations. The occupancy of each conformation was
adjusted so as to result in approximately equal mean
thermal factors for the atoms in each conformation.</VRPTx:details>
<VRPTx:treatment>fix</VRPTx:treatment>
<VRPTx:value>0.35</VRPTx:value>
</VRPTx:refine_occupancy>
</VRPTx:refine_occupancyCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refine_occupancy.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | reflnType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFLN category record details about the
reflection data used to determine the ATOM_SITE data items.
The REFLN data items refer to individual reflections and must
be included in looped lists.
The REFLNS data items specify the parameters that apply to all
reflections. The REFLNS data items are not looped.
Example 1 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov
[Acta Cryst. (1993), C49, 1352-1354].
<VRPTx:reflnCategory>
<VRPTx:refln index_h="2" index_k="0" index_l="0">
<VRPTx:F_squared_calc>85.57</VRPTx:F_squared_calc>
<VRPTx:F_squared_meas>58.90</VRPTx:F_squared_meas>
<VRPTx:F_squared_sigma>1.45</VRPTx:F_squared_sigma>
<VRPTx:status>o</VRPTx:status>
</VRPTx:refln>
<VRPTx:refln index_h="3" index_k="0" index_l="0">
<VRPTx:F_squared_calc>15718.18</VRPTx:F_squared_calc>
<VRPTx:F_squared_meas>15631.06</VRPTx:F_squared_meas>
<VRPTx:F_squared_sigma>30.40</VRPTx:F_squared_sigma>
<VRPTx:status>o</VRPTx:status>
</VRPTx:refln>
<VRPTx:refln index_h="4" index_k="0" index_l="0">
<VRPTx:F_squared_calc>55613.11</VRPTx:F_squared_calc>
<VRPTx:F_squared_meas>49840.09</VRPTx:F_squared_meas>
<VRPTx:F_squared_sigma>61.86</VRPTx:F_squared_sigma>
<VRPTx:status>o</VRPTx:status>
</VRPTx:refln>
<VRPTx:refln index_h="5" index_k="0" index_l="0">
<VRPTx:F_squared_calc>246.85</VRPTx:F_squared_calc>
<VRPTx:F_squared_meas>241.86</VRPTx:F_squared_meas>
<VRPTx:F_squared_sigma>10.02</VRPTx:F_squared_sigma>
<VRPTx:status>o</VRPTx:status>
</VRPTx:refln>
<VRPTx:refln index_h="6" index_k="0" index_l="0">
<VRPTx:F_squared_calc>82.16</VRPTx:F_squared_calc>
<VRPTx:F_squared_meas>69.97</VRPTx:F_squared_meas>
<VRPTx:F_squared_sigma>1.93</VRPTx:F_squared_sigma>
<VRPTx:status>o</VRPTx:status>
</VRPTx:refln>
<VRPTx:refln index_h="7" index_k="0" index_l="0">
<VRPTx:F_squared_calc>1133.62</VRPTx:F_squared_calc>
<VRPTx:F_squared_meas>947.79</VRPTx:F_squared_meas>
<VRPTx:F_squared_sigma>11.78</VRPTx:F_squared_sigma>
<VRPTx:status>o</VRPTx:status>
</VRPTx:refln>
<VRPTx:refln index_h="8" index_k="0" index_l="0">
<VRPTx:F_squared_calc>2558.04</VRPTx:F_squared_calc>
<VRPTx:F_squared_meas>2453.33</VRPTx:F_squared_meas>
<VRPTx:F_squared_sigma>20.44</VRPTx:F_squared_sigma>
<VRPTx:status>o</VRPTx:status>
</VRPTx:refln>
<VRPTx:refln index_h="9" index_k="0" index_l="0">
<VRPTx:F_squared_calc>283.88</VRPTx:F_squared_calc>
<VRPTx:F_squared_meas>393.66</VRPTx:F_squared_meas>
<VRPTx:F_squared_sigma>7.79</VRPTx:F_squared_sigma>
<VRPTx:status>o</VRPTx:status>
</VRPTx:refln>
<VRPTx:refln index_h="10" index_k="0" index_l="0">
<VRPTx:F_squared_calc>283.70</VRPTx:F_squared_calc>
<VRPTx:F_squared_meas>171.98</VRPTx:F_squared_meas>
<VRPTx:F_squared_sigma>4.26</VRPTx:F_squared_sigma>
<VRPTx:status>o</VRPTx:status>
</VRPTx:refln>
</VRPTx:reflnCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refln.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | refln_sys_absType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFLN_SYS_ABS category record details about
the reflection data that should be systematically absent,
given the designated space group.
Example 1 - hypothetical example.
<VRPTx:refln_sys_absCategory>
<VRPTx:refln_sys_abs index_h="0" index_k="3" index_l="0">
<VRPTx:I>28.32</VRPTx:I>
<VRPTx:I_over_sigmaI>1.23</VRPTx:I_over_sigmaI>
<VRPTx:sigmaI>22.95</VRPTx:sigmaI>
</VRPTx:refln_sys_abs>
<VRPTx:refln_sys_abs index_h="0" index_k="5" index_l="0">
<VRPTx:I>14.11</VRPTx:I>
<VRPTx:I_over_sigmaI>0.86</VRPTx:I_over_sigmaI>
<VRPTx:sigmaI>16.38</VRPTx:sigmaI>
</VRPTx:refln_sys_abs>
<VRPTx:refln_sys_abs index_h="0" index_k="7" index_l="0">
<VRPTx:I>114.81</VRPTx:I>
<VRPTx:I_over_sigmaI>5.67</VRPTx:I_over_sigmaI>
<VRPTx:sigmaI>20.22</VRPTx:sigmaI>
</VRPTx:refln_sys_abs>
<VRPTx:refln_sys_abs index_h="0" index_k="9" index_l="0">
<VRPTx:I>32.99</VRPTx:I>
<VRPTx:I_over_sigmaI>1.35</VRPTx:I_over_sigmaI>
<VRPTx:sigmaI>24.51</VRPTx:sigmaI>
</VRPTx:refln_sys_abs>
</VRPTx:refln_sys_absCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/refln_sys_abs.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | reflnsType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFLNS category record details about the
reflection data used to determine the ATOM_SITE data items.
The REFLN data items refer to individual reflections and must
be included in looped lists.
The REFLNS data items specify the parameters that apply to all
reflections. The REFLNS data items are not looped.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:reflnsCategory>
<VRPTx:reflns pdbx_ordinal="1">
<VRPTx:d_resolution_high>2.00</VRPTx:d_resolution_high>
<VRPTx:d_resolution_low>8.00</VRPTx:d_resolution_low>
<VRPTx:data_reduction_details> Merging and scaling based on only those reflections
with I > \s(I).</VRPTx:data_reduction_details>
<VRPTx:data_reduction_method> Xengen program scalei. Anomalous pairs were merged. Scaling
proceeded in several passes, beginning with 1-parameter
fit and ending with 3-parameter fit.</VRPTx:data_reduction_method>
<VRPTx:details>none</VRPTx:details>
<VRPTx:entry_id>5HVP</VRPTx:entry_id>
<VRPTx:limit_h_max>22</VRPTx:limit_h_max>
<VRPTx:limit_h_min>0</VRPTx:limit_h_min>
<VRPTx:limit_k_max>46</VRPTx:limit_k_max>
<VRPTx:limit_k_min>0</VRPTx:limit_k_min>
<VRPTx:limit_l_max>57</VRPTx:limit_l_max>
<VRPTx:limit_l_min>0</VRPTx:limit_l_min>
<VRPTx:number_obs>7228</VRPTx:number_obs>
<VRPTx:observed_criterion>> 1 \s(I)</VRPTx:observed_criterion>
<VRPTx:pdbx_diffrn_id>1</VRPTx:pdbx_diffrn_id>
</VRPTx:reflns>
</VRPTx:reflnsCategory>
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
<VRPTx:reflnsCategory>
<VRPTx:reflns pdbx_ordinal="1">
<VRPTx:d_resolution_high>0.8733</VRPTx:d_resolution_high>
<VRPTx:d_resolution_low>11.9202</VRPTx:d_resolution_low>
<VRPTx:entry_id>1TOZ</VRPTx:entry_id>
<VRPTx:limit_h_max>6</VRPTx:limit_h_max>
<VRPTx:limit_h_min>0</VRPTx:limit_h_min>
<VRPTx:limit_k_max>17</VRPTx:limit_k_max>
<VRPTx:limit_k_min>0</VRPTx:limit_k_min>
<VRPTx:limit_l_max>22</VRPTx:limit_l_max>
<VRPTx:limit_l_min>0</VRPTx:limit_l_min>
<VRPTx:number_all>1592</VRPTx:number_all>
<VRPTx:number_obs>1408</VRPTx:number_obs>
<VRPTx:observed_criterion>F_>_6.0_\s(F)</VRPTx:observed_criterion>
<VRPTx:pdbx_diffrn_id>1</VRPTx:pdbx_diffrn_id>
</VRPTx:reflns>
</VRPTx:reflnsCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/reflns.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | reflns_classType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFLNS_CLASS category record details
of the reflections used to determine the structural
parameters for each reflection class.
Example 1 - example corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
<VRPTx:reflns_classCategory>
<VRPTx:reflns_class code="Main">
<VRPTx:number_gt>584</VRPTx:number_gt>
</VRPTx:reflns_class>
<VRPTx:reflns_class code="Sat1">
<VRPTx:number_gt>226</VRPTx:number_gt>
</VRPTx:reflns_class>
<VRPTx:reflns_class code="Sat2">
<VRPTx:number_gt>50</VRPTx:number_gt>
</VRPTx:reflns_class>
</VRPTx:reflns_classCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/reflns_class.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | reflns_scaleType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFLNS_SCALE category record details about
the structure-factor scales. They are referenced from within
the REFLN list through attribute scale_group_code in category refln.
Example 1 - based on laboratory records for the collagen-like
peptide [(POG)4 EKG (POG)5]3.
<VRPTx:reflns_scaleCategory>
<VRPTx:reflns_scale group_code="SG1">
<VRPTx:meas_F>4.0</VRPTx:meas_F>
</VRPTx:reflns_scale>
</VRPTx:reflns_scaleCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/reflns_scale.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | reflns_shellType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the REFLNS_SHELL category record details about
the reflection data used to determine the ATOM_SITE data items
broken down into shells of resolution.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:reflns_shellCategory>
<VRPTx:reflns_shell pdbx_ordinal="1">
<VRPTx:Rmerge_F_obs>1.98</VRPTx:Rmerge_F_obs>
<VRPTx:d_res_high>31.38</VRPTx:d_res_high>
<VRPTx:d_res_low>3.82</VRPTx:d_res_low>
<VRPTx:meanI_over_sigI_obs>69.8</VRPTx:meanI_over_sigI_obs>
<VRPTx:number_measured_obs>9024</VRPTx:number_measured_obs>
<VRPTx:number_unique_obs>2540</VRPTx:number_unique_obs>
<VRPTx:percent_possible_obs>96.8</VRPTx:percent_possible_obs>
</VRPTx:reflns_shell>
<VRPTx:reflns_shell pdbx_ordinal="2">
<VRPTx:Rmerge_F_obs>3.85</VRPTx:Rmerge_F_obs>
<VRPTx:d_res_high>3.82</VRPTx:d_res_high>
<VRPTx:d_res_low>3.03</VRPTx:d_res_low>
<VRPTx:meanI_over_sigI_obs>26.1</VRPTx:meanI_over_sigI_obs>
<VRPTx:number_measured_obs>7413</VRPTx:number_measured_obs>
<VRPTx:number_unique_obs>2364</VRPTx:number_unique_obs>
<VRPTx:percent_possible_obs>95.1</VRPTx:percent_possible_obs>
</VRPTx:reflns_shell>
<VRPTx:reflns_shell pdbx_ordinal="3">
<VRPTx:Rmerge_F_obs>6.37</VRPTx:Rmerge_F_obs>
<VRPTx:d_res_high>3.03</VRPTx:d_res_high>
<VRPTx:d_res_low>2.65</VRPTx:d_res_low>
<VRPTx:meanI_over_sigI_obs>10.5</VRPTx:meanI_over_sigI_obs>
<VRPTx:number_measured_obs>5640</VRPTx:number_measured_obs>
<VRPTx:number_unique_obs>2123</VRPTx:number_unique_obs>
<VRPTx:percent_possible_obs>86.2</VRPTx:percent_possible_obs>
</VRPTx:reflns_shell>
<VRPTx:reflns_shell pdbx_ordinal="4">
<VRPTx:Rmerge_F_obs>8.01</VRPTx:Rmerge_F_obs>
<VRPTx:d_res_high>2.65</VRPTx:d_res_high>
<VRPTx:d_res_low>2.41</VRPTx:d_res_low>
<VRPTx:meanI_over_sigI_obs>6.4</VRPTx:meanI_over_sigI_obs>
<VRPTx:number_measured_obs>4322</VRPTx:number_measured_obs>
<VRPTx:number_unique_obs>1882</VRPTx:number_unique_obs>
<VRPTx:percent_possible_obs>76.8</VRPTx:percent_possible_obs>
</VRPTx:reflns_shell>
<VRPTx:reflns_shell pdbx_ordinal="5">
<VRPTx:Rmerge_F_obs>9.86</VRPTx:Rmerge_F_obs>
<VRPTx:d_res_high>2.41</VRPTx:d_res_high>
<VRPTx:d_res_low>2.23</VRPTx:d_res_low>
<VRPTx:meanI_over_sigI_obs>4.3</VRPTx:meanI_over_sigI_obs>
<VRPTx:number_measured_obs>3247</VRPTx:number_measured_obs>
<VRPTx:number_unique_obs>1714</VRPTx:number_unique_obs>
<VRPTx:percent_possible_obs>70.4</VRPTx:percent_possible_obs>
</VRPTx:reflns_shell>
<VRPTx:reflns_shell pdbx_ordinal="6">
<VRPTx:Rmerge_F_obs>13.99</VRPTx:Rmerge_F_obs>
<VRPTx:d_res_high>2.23</VRPTx:d_res_high>
<VRPTx:d_res_low>2.10</VRPTx:d_res_low>
<VRPTx:meanI_over_sigI_obs>3.1</VRPTx:meanI_over_sigI_obs>
<VRPTx:number_measured_obs>1140</VRPTx:number_measured_obs>
<VRPTx:number_unique_obs>812</VRPTx:number_unique_obs>
<VRPTx:percent_possible_obs>33.3</VRPTx:percent_possible_obs>
</VRPTx:reflns_shell>
</VRPTx:reflns_shellCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/reflns_shell.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | space_groupType |
|---|---|
| Abstract | no |
| Documentation |
Contains all the data items that refer to the space group as a
whole, such as its name or crystal system. They may be looped,
for example, in a list of space groups and their properties.
Only a subset of the SPACE_GROUP category items appear in
this dictionary. The remainder are found in the symmetry CIF
dictionary.
Space-group types are identified by their number as given in
International Tables for Crystallography Vol. A. Specific
settings of the space groups can be identified either by their
Hall symbol or by specifying their symmetry operations.
The commonly used Hermann-Mauguin symbol determines the
space-group type uniquely but several different Hermann-Mauguin
symbols may refer to the same space-group type. A Hermann-Mauguin
symbol contains information on the choice of the basis, but not
on the choice of origin. Different formats for the
Hermann-Mauguin symbol are found in the symmetry CIF dictionary.
Example 1 - the monoclinic space group No. 15 with unique axis b.
<VRPTx:space_groupCategory>
<VRPTx:space_group id="1">
<VRPTx:IT_number>15</VRPTx:IT_number>
<VRPTx:crystal_system>monoclinic</VRPTx:crystal_system>
<VRPTx:name_H-M_alt>C 2/c</VRPTx:name_H-M_alt>
<VRPTx:name_Hall>-C 2yc</VRPTx:name_Hall>
</VRPTx:space_group>
</VRPTx:space_groupCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/space_group.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | space_group_symopType |
|---|---|
| Abstract | no |
| Documentation |
Contains information about the symmetry operations of the
space group.
Example 1 - The symmetry operations for the space group P21/c.
<VRPTx:space_group_symopCategory>
<VRPTx:space_group_symop id="1">
<VRPTx:operation_xyz>x,y,z</VRPTx:operation_xyz>
</VRPTx:space_group_symop>
<VRPTx:space_group_symop id="2">
<VRPTx:operation_xyz>-x,-y,-z</VRPTx:operation_xyz>
</VRPTx:space_group_symop>
<VRPTx:space_group_symop id="3">
<VRPTx:operation_xyz>-x,1/2+y,1/2-z</VRPTx:operation_xyz>
</VRPTx:space_group_symop>
<VRPTx:space_group_symop id="4">
<VRPTx:operation_xyz>x,1/2-y,1/2+z</VRPTx:operation_xyz>
</VRPTx:space_group_symop>
</VRPTx:space_group_symopCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/space_group_symop.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | structType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT category record details about the
description of the crystallographic structure.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:structCategory>
<VRPTx:struct entry_id="5HVP">
<VRPTx:title> HIV-1 protease complex with acetyl-pepstatin</VRPTx:title>
</VRPTx:struct>
</VRPTx:structCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_asymType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_ASYM category record details about the
structural elements in the asymmetric unit.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:struct_asymCategory>
<VRPTx:struct_asym id="A">
<VRPTx:details>one monomer of the dimeric enzyme</VRPTx:details>
<VRPTx:entity_id>1</VRPTx:entity_id>
</VRPTx:struct_asym>
<VRPTx:struct_asym id="B">
<VRPTx:details>one monomer of the dimeric enzyme</VRPTx:details>
<VRPTx:entity_id>1</VRPTx:entity_id>
</VRPTx:struct_asym>
<VRPTx:struct_asym id="C">
<VRPTx:details>one partially occupied position for the inhibitor</VRPTx:details>
<VRPTx:entity_id>2</VRPTx:entity_id>
</VRPTx:struct_asym>
<VRPTx:struct_asym id="D">
<VRPTx:details>one partially occupied position for the inhibitor</VRPTx:details>
<VRPTx:entity_id>2</VRPTx:entity_id>
</VRPTx:struct_asym>
</VRPTx:struct_asymCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_asym.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_biolType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_BIOL category record details about
the structural elements that form each structure of biological
significance.
A given crystal structure may contain many different biological
structures. A given structural component in the asymmetric
unit may be part of more than one biological unit. A given
biological structure may involve crystallographic symmetry.
For instance, in a structure of a lysozyme-FAB structure, the
light- and heavy-chain components of the FAB could be one
biological unit, while the two chains of the FAB and the lysozyme
could constitute a second biological unit.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:struct_biolCategory>
<VRPTx:struct_biol id="1">
<VRPTx:details> significant deviations from twofold symmetry exist in this
dimeric enzyme</VRPTx:details>
</VRPTx:struct_biol>
<VRPTx:struct_biol id="2">
<VRPTx:details> The drug binds to this enzyme in two roughly twofold
symmetric modes. Hence this biological unit (2) is roughly
twofold symmetric to biological unit (3). Disorder in the
protein chain indicated with alternative ID 1 should be
used with this biological unit.</VRPTx:details>
</VRPTx:struct_biol>
<VRPTx:struct_biol id="3">
<VRPTx:details> The drug binds to this enzyme in two roughly twofold
symmetric modes. Hence this biological unit (3) is roughly
twofold symmetric to biological unit (2). Disorder in the
protein chain indicated with alternative ID 2 should be
used with this biological unit.</VRPTx:details>
</VRPTx:struct_biol>
</VRPTx:struct_biolCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_biol.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_biol_viewType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_BIOL_VIEW category record details
about how to draw and annotate an informative view of the
biological structure.
Example 1 - based on NDB structure GDL001 by Coll, Aymami,
Van Der Marel, Van Boom, Rich & Wang
[Biochemistry, (1989), 28, 310-320].
<VRPTx:struct_biol_viewCategory>
<VRPTx:struct_biol_view biol_id="c1" id="1">
<VRPTx:details> This view highlights the ATAT-Netropsin interaction in the
DNA-drug complex.</VRPTx:details>
<VRPTx:rot_matrix11>0.132</VRPTx:rot_matrix11>
<VRPTx:rot_matrix12>0.922</VRPTx:rot_matrix12>
<VRPTx:rot_matrix13>-0.363</VRPTx:rot_matrix13>
<VRPTx:rot_matrix21>0.131</VRPTx:rot_matrix21>
<VRPTx:rot_matrix22>-0.380</VRPTx:rot_matrix22>
<VRPTx:rot_matrix23>-0.916</VRPTx:rot_matrix23>
<VRPTx:rot_matrix31>-0.982</VRPTx:rot_matrix31>
<VRPTx:rot_matrix32>0.073</VRPTx:rot_matrix32>
<VRPTx:rot_matrix33>-0.172</VRPTx:rot_matrix33>
</VRPTx:struct_biol_view>
</VRPTx:struct_biol_viewCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_biol_view.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_confType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_CONF category record details about
the backbone conformation of a segment of polymer.
Data items in the STRUCT_CONF_TYPE category define the
criteria used to identify the backbone conformations.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:struct_confCategory>
<VRPTx:struct_conf id="HELX1">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ARG</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>87</VRPTx:beg_label_seq_id>
<VRPTx:conf_type_id>HELX_RH_AL_P</VRPTx:conf_type_id>
<VRPTx:details xsi:nil="true" />
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>GLN</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>92</VRPTx:end_label_seq_id>
</VRPTx:struct_conf>
<VRPTx:struct_conf id="HELX2">
<VRPTx:beg_label_asym_id>B</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ARG</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>287</VRPTx:beg_label_seq_id>
<VRPTx:conf_type_id>HELX_RH_AL_P</VRPTx:conf_type_id>
<VRPTx:details xsi:nil="true" />
<VRPTx:end_label_asym_id>B</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>GLN</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>292</VRPTx:end_label_seq_id>
</VRPTx:struct_conf>
<VRPTx:struct_conf id="STRN1">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>1</VRPTx:beg_label_seq_id>
<VRPTx:conf_type_id>STRN_P</VRPTx:conf_type_id>
<VRPTx:details xsi:nil="true" />
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>LEU</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>5</VRPTx:end_label_seq_id>
</VRPTx:struct_conf>
<VRPTx:struct_conf id="STRN2">
<VRPTx:beg_label_asym_id>B</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>CYS</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>295</VRPTx:beg_label_seq_id>
<VRPTx:conf_type_id>STRN_P</VRPTx:conf_type_id>
<VRPTx:details xsi:nil="true" />
<VRPTx:end_label_asym_id>B</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>PHE</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>299</VRPTx:end_label_seq_id>
</VRPTx:struct_conf>
<VRPTx:struct_conf id="STRN3">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>CYS</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>95</VRPTx:beg_label_seq_id>
<VRPTx:conf_type_id>STRN_P</VRPTx:conf_type_id>
<VRPTx:details xsi:nil="true" />
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>PHE</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>299</VRPTx:end_label_seq_id>
</VRPTx:struct_conf>
<VRPTx:struct_conf id="STRN4">
<VRPTx:beg_label_asym_id>B</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>201</VRPTx:beg_label_seq_id>
<VRPTx:conf_type_id>STRN_P</VRPTx:conf_type_id>
<VRPTx:details xsi:nil="true" />
<VRPTx:end_label_asym_id>B</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>LEU</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>205</VRPTx:end_label_seq_id>
</VRPTx:struct_conf>
<VRPTx:struct_conf id="TURN1">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ILE</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>15</VRPTx:beg_label_seq_id>
<VRPTx:conf_type_id>TURN_TY1P_P</VRPTx:conf_type_id>
<VRPTx:details xsi:nil="true" />
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>GLN</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>18</VRPTx:end_label_seq_id>
</VRPTx:struct_conf>
<VRPTx:struct_conf id="TURN2">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>GLY</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>49</VRPTx:beg_label_seq_id>
<VRPTx:conf_type_id>TURN_TY2_P</VRPTx:conf_type_id>
<VRPTx:details xsi:nil="true" />
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>52</VRPTx:end_label_seq_id>
</VRPTx:struct_conf>
<VRPTx:struct_conf id="TURN3">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ILE</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>55</VRPTx:beg_label_seq_id>
<VRPTx:conf_type_id>TURN_TY1P_P</VRPTx:conf_type_id>
<VRPTx:details xsi:nil="true" />
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>HIS</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>69</VRPTx:end_label_seq_id>
</VRPTx:struct_conf>
<VRPTx:struct_conf id="TURN4">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>THR</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>91</VRPTx:beg_label_seq_id>
<VRPTx:conf_type_id>TURN_TY1_P</VRPTx:conf_type_id>
<VRPTx:details xsi:nil="true" />
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>94</VRPTx:end_label_seq_id>
</VRPTx:struct_conf>
</VRPTx:struct_confCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_conf.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_conf_typeType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_CONF_TYPE category record details
about the criteria used to identify backbone conformations of a
segment of polymer.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:struct_conf_typeCategory>
<VRPTx:struct_conf_type id="HELX_RH_AL_P">
<VRPTx:criteria>author judgement</VRPTx:criteria>
<VRPTx:reference xsi:nil="true" />
</VRPTx:struct_conf_type>
<VRPTx:struct_conf_type id="STRN_P">
<VRPTx:criteria>author judgement</VRPTx:criteria>
<VRPTx:reference xsi:nil="true" />
</VRPTx:struct_conf_type>
<VRPTx:struct_conf_type id="TURN_TY1_P">
<VRPTx:criteria>author judgement</VRPTx:criteria>
<VRPTx:reference xsi:nil="true" />
</VRPTx:struct_conf_type>
<VRPTx:struct_conf_type id="TURN_TY1P_P">
<VRPTx:criteria>author judgement</VRPTx:criteria>
<VRPTx:reference xsi:nil="true" />
</VRPTx:struct_conf_type>
<VRPTx:struct_conf_type id="TURN_TY2_P">
<VRPTx:criteria>author judgement</VRPTx:criteria>
<VRPTx:reference xsi:nil="true" />
</VRPTx:struct_conf_type>
<VRPTx:struct_conf_type id="TURN_TY2P_P">
<VRPTx:criteria>author judgement</VRPTx:criteria>
<VRPTx:reference xsi:nil="true" />
</VRPTx:struct_conf_type>
</VRPTx:struct_conf_typeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_conf_type.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_connType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_CONN category record details about
the connections between portions of the structure. These can be
hydrogen bonds, salt bridges, disulfide bridges and so on.
The STRUCT_CONN_TYPE records define the criteria used to
identify these connections.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:struct_connCategory>
<VRPTx:struct_conn id="C1">
<VRPTx:conn_type_id>saltbr</VRPTx:conn_type_id>
<VRPTx:details xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>A</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>NZ1</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>ARG</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>87</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr1_role>positive</VRPTx:ptnr1_role>
<VRPTx:ptnr1_symmetry>1_555</VRPTx:ptnr1_symmetry>
<VRPTx:ptnr2_label_asym_id>A</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id>OE1</VRPTx:ptnr2_label_atom_id>
<VRPTx:ptnr2_label_comp_id>GLU</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>92</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr2_role>negative</VRPTx:ptnr2_role>
<VRPTx:ptnr2_symmetry>1_555</VRPTx:ptnr2_symmetry>
</VRPTx:struct_conn>
<VRPTx:struct_conn id="C2">
<VRPTx:conn_type_id>hydrog</VRPTx:conn_type_id>
<VRPTx:details xsi:nil="true" />
<VRPTx:ptnr1_label_asym_id>B</VRPTx:ptnr1_label_asym_id>
<VRPTx:ptnr1_label_atom_id>N</VRPTx:ptnr1_label_atom_id>
<VRPTx:ptnr1_label_comp_id>ARG</VRPTx:ptnr1_label_comp_id>
<VRPTx:ptnr1_label_seq_id>287</VRPTx:ptnr1_label_seq_id>
<VRPTx:ptnr1_role>donor</VRPTx:ptnr1_role>
<VRPTx:ptnr1_symmetry>1_555</VRPTx:ptnr1_symmetry>
<VRPTx:ptnr2_label_asym_id>B</VRPTx:ptnr2_label_asym_id>
<VRPTx:ptnr2_label_atom_id>O</VRPTx:ptnr2_label_atom_id>
<VRPTx:ptnr2_label_comp_id>GLY</VRPTx:ptnr2_label_comp_id>
<VRPTx:ptnr2_label_seq_id>292</VRPTx:ptnr2_label_seq_id>
<VRPTx:ptnr2_role>acceptor</VRPTx:ptnr2_role>
<VRPTx:ptnr2_symmetry>1_555</VRPTx:ptnr2_symmetry>
</VRPTx:struct_conn>
</VRPTx:struct_connCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_conn.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_conn_typeType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_CONN_TYPE category record details
about the criteria used to identify interactions between
portions of the structure.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:struct_conn_typeCategory>
<VRPTx:struct_conn_type id="saltbr">
<VRPTx:criteria>negative to positive distance > 2.5 \%A, < 3.2 \%A</VRPTx:criteria>
<VRPTx:reference xsi:nil="true" />
</VRPTx:struct_conn_type>
<VRPTx:struct_conn_type id="hydrog">
<VRPTx:criteria>NO distance > 2.5\%A, < 3.5\%A, NOC angle < 120 degrees</VRPTx:criteria>
<VRPTx:reference xsi:nil="true" />
</VRPTx:struct_conn_type>
</VRPTx:struct_conn_typeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_conn_type.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_mon_detailsType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_MON_DETAILS category record details
about specifics of calculations summarized in data items in the
STRUCT_MON_PROT and STRUCT_MON_NUCL categories. These can
include the coefficients used in map calculations,
the radii used for including points in a calculation and so on.
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_mon_details.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_mon_nuclType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_MON_NUCL category record details about
structural properties of a nucleic acid when analyzed at the
monomer level. Analogous data items for proteins are given in
the STRUCT_MON_PROT category. For items where the value of the
property depends on the method employed to calculate it,
details of the method of calculation are given using data items
in the STRUCT_MON_DETAILS category.
Example 1 - based on NDB structure BDL028.
<VRPTx:struct_mon_nuclCategory>
<VRPTx:struct_mon_nucl pdbx_id="1">
<VRPTx:alpha xsi:nil="true" />
<VRPTx:beta xsi:nil="true" />
<VRPTx:delta>131.9</VRPTx:delta>
<VRPTx:epsilon>222.1</VRPTx:epsilon>
<VRPTx:gamma>29.9</VRPTx:gamma>
<VRPTx:label_alt_id>A</VRPTx:label_alt_id>
<VRPTx:label_asym_id>A</VRPTx:label_asym_id>
<VRPTx:label_comp_id>C</VRPTx:label_comp_id>
<VRPTx:label_seq_id>1</VRPTx:label_seq_id>
<VRPTx:zeta>174.2</VRPTx:zeta>
</VRPTx:struct_mon_nucl>
<VRPTx:struct_mon_nucl pdbx_id="2">
<VRPTx:alpha>334.0</VRPTx:alpha>
<VRPTx:beta>130.6</VRPTx:beta>
<VRPTx:delta>125.6</VRPTx:delta>
<VRPTx:epsilon>167.6</VRPTx:epsilon>
<VRPTx:gamma>33.1</VRPTx:gamma>
<VRPTx:label_alt_id>A</VRPTx:label_alt_id>
<VRPTx:label_asym_id>A</VRPTx:label_asym_id>
<VRPTx:label_comp_id>G</VRPTx:label_comp_id>
<VRPTx:label_seq_id>2</VRPTx:label_seq_id>
<VRPTx:zeta>270.9</VRPTx:zeta>
</VRPTx:struct_mon_nucl>
<VRPTx:struct_mon_nucl pdbx_id="3">
<VRPTx:alpha>258.2</VRPTx:alpha>
<VRPTx:beta>178.7</VRPTx:beta>
<VRPTx:delta>114.6</VRPTx:delta>
<VRPTx:epsilon>216.6</VRPTx:epsilon>
<VRPTx:gamma>101.0</VRPTx:gamma>
<VRPTx:label_alt_id>A</VRPTx:label_alt_id>
<VRPTx:label_asym_id>A</VRPTx:label_asym_id>
<VRPTx:label_comp_id>T</VRPTx:label_comp_id>
<VRPTx:label_seq_id>3</VRPTx:label_seq_id>
<VRPTx:zeta>259.3</VRPTx:zeta>
</VRPTx:struct_mon_nucl>
</VRPTx:struct_mon_nuclCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_mon_nucl.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_mon_protType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_MON_PROT category record details about
structural properties of a protein when analyzed at the monomer
level. Analogous data items for nucleic acids are given in the
STRUCT_MON_NUCL category. For items where the value of the
property depends on the method employed to calculate it,
details of the method of calculation are given using data items
in the STRUCT_MON_DETAILS category.
Example 1 - based on laboratory records for protein NS1.
This example provides details for residue ARG 35.
<VRPTx:struct_mon_protCategory>
<VRPTx:struct_mon_prot pdbx_id="1">
<VRPTx:RSCC_all>0.90</VRPTx:RSCC_all>
<VRPTx:RSR_all>0.18</VRPTx:RSR_all>
<VRPTx:chi1>-67.9</VRPTx:chi1>
<VRPTx:chi2>-174.7</VRPTx:chi2>
<VRPTx:chi3>-67.7</VRPTx:chi3>
<VRPTx:chi4>-86.3</VRPTx:chi4>
<VRPTx:chi5>4.2</VRPTx:chi5>
<VRPTx:label_alt_id>A</VRPTx:label_alt_id>
<VRPTx:label_asym_id>A</VRPTx:label_asym_id>
<VRPTx:label_comp_id>ARG</VRPTx:label_comp_id>
<VRPTx:label_seq_id>35</VRPTx:label_seq_id>
<VRPTx:mean_B_all>30.0</VRPTx:mean_B_all>
<VRPTx:mean_B_main>25.0</VRPTx:mean_B_main>
<VRPTx:mean_B_side>35.1</VRPTx:mean_B_side>
<VRPTx:omega>180.1</VRPTx:omega>
<VRPTx:phi>-60.3</VRPTx:phi>
<VRPTx:psi>-46.0</VRPTx:psi>
</VRPTx:struct_mon_prot>
</VRPTx:struct_mon_protCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_mon_prot.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_mon_prot_cisType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_MON_PROT_CIS category identify
monomers that have been found to have the peptide bond in the cis
conformation. The criterion used to select residues to be
designated as containing cis peptide bonds is given in
attribute prot_cis in category struct_mon_details.
Example 1 - based on PDB structure 1ACY of Ghiara, Stura, Stanfield,
Profy & Wilson [Science (1994), 264, 82-85].
<VRPTx:struct_mon_prot_cisCategory>
<VRPTx:struct_mon_prot_cis pdbx_id="1">
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:label_asym_id>L</VRPTx:label_asym_id>
<VRPTx:label_comp_id>PRO</VRPTx:label_comp_id>
<VRPTx:label_seq_id>8</VRPTx:label_seq_id>
<VRPTx:pdbx_PDB_model_num>1</VRPTx:pdbx_PDB_model_num>
</VRPTx:struct_mon_prot_cis>
<VRPTx:struct_mon_prot_cis pdbx_id="2">
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:label_asym_id>L</VRPTx:label_asym_id>
<VRPTx:label_comp_id>PRO</VRPTx:label_comp_id>
<VRPTx:label_seq_id>77</VRPTx:label_seq_id>
<VRPTx:pdbx_PDB_model_num>1</VRPTx:pdbx_PDB_model_num>
</VRPTx:struct_mon_prot_cis>
<VRPTx:struct_mon_prot_cis pdbx_id="3">
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:label_asym_id>L</VRPTx:label_asym_id>
<VRPTx:label_comp_id>PRO</VRPTx:label_comp_id>
<VRPTx:label_seq_id>95</VRPTx:label_seq_id>
<VRPTx:pdbx_PDB_model_num>1</VRPTx:pdbx_PDB_model_num>
</VRPTx:struct_mon_prot_cis>
<VRPTx:struct_mon_prot_cis pdbx_id="4">
<VRPTx:label_alt_id xsi:nil="true" />
<VRPTx:label_asym_id>L</VRPTx:label_asym_id>
<VRPTx:label_comp_id>PRO</VRPTx:label_comp_id>
<VRPTx:label_seq_id>141</VRPTx:label_seq_id>
<VRPTx:pdbx_PDB_model_num>1</VRPTx:pdbx_PDB_model_num>
</VRPTx:struct_mon_prot_cis>
</VRPTx:struct_mon_prot_cisCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_mon_prot_cis.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_ncs_domType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_NCS_DOM category record information
about the domains in an ensemble of domains related by one or
more noncrystallographic symmetry operators.
A domain need not correspond to a complete polypeptide chain;
it can be composed of one or more segments in a single chain,
or by segments from more than one chain.
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
<VRPTx:struct_ncs_domCategory>
<VRPTx:struct_ncs_dom id="d1" pdbx_ens_id="1">
<VRPTx:details>Chains A, B, and C</VRPTx:details>
</VRPTx:struct_ncs_dom>
<VRPTx:struct_ncs_dom id="d2" pdbx_ens_id="1">
<VRPTx:details>Chains D, E, and F</VRPTx:details>
</VRPTx:struct_ncs_dom>
</VRPTx:struct_ncs_domCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_ncs_dom.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_ncs_dom_limType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_NCS_DOM_LIM category identify the
start and end points of polypeptide chain segments
that form all or part of a domain in an ensemble of domains
related by noncrystallographic symmetry.
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
<VRPTx:struct_ncs_dom_limCategory>
<VRPTx:struct_ncs_dom_lim dom_id="d1" pdbx_component_id="1" pdbx_ens_id="1">
<VRPTx:beg_label_alt_id xsi:nil="true" />
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>1</VRPTx:beg_label_seq_id>
<VRPTx:end_label_alt_id xsi:nil="true" />
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>29</VRPTx:end_label_seq_id>
</VRPTx:struct_ncs_dom_lim>
<VRPTx:struct_ncs_dom_lim dom_id="d1" pdbx_component_id="2" pdbx_ens_id="1">
<VRPTx:beg_label_alt_id xsi:nil="true" />
<VRPTx:beg_label_asym_id>B</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>31</VRPTx:beg_label_seq_id>
<VRPTx:end_label_alt_id xsi:nil="true" />
<VRPTx:end_label_asym_id>B</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>59</VRPTx:end_label_seq_id>
</VRPTx:struct_ncs_dom_lim>
<VRPTx:struct_ncs_dom_lim dom_id="d1" pdbx_component_id="3" pdbx_ens_id="1">
<VRPTx:beg_label_alt_id xsi:nil="true" />
<VRPTx:beg_label_asym_id>C</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>61</VRPTx:beg_label_seq_id>
<VRPTx:end_label_alt_id xsi:nil="true" />
<VRPTx:end_label_asym_id>B</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>89</VRPTx:end_label_seq_id>
</VRPTx:struct_ncs_dom_lim>
<VRPTx:struct_ncs_dom_lim dom_id="d2" pdbx_component_id="1" pdbx_ens_id="1">
<VRPTx:beg_label_alt_id xsi:nil="true" />
<VRPTx:beg_label_asym_id>D</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>91</VRPTx:beg_label_seq_id>
<VRPTx:end_label_alt_id xsi:nil="true" />
<VRPTx:end_label_asym_id>D</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>119</VRPTx:end_label_seq_id>
</VRPTx:struct_ncs_dom_lim>
<VRPTx:struct_ncs_dom_lim dom_id="d2" pdbx_component_id="2" pdbx_ens_id="1">
<VRPTx:beg_label_alt_id xsi:nil="true" />
<VRPTx:beg_label_asym_id>E</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>121</VRPTx:beg_label_seq_id>
<VRPTx:end_label_alt_id xsi:nil="true" />
<VRPTx:end_label_asym_id>E</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>149</VRPTx:end_label_seq_id>
</VRPTx:struct_ncs_dom_lim>
<VRPTx:struct_ncs_dom_lim dom_id="d2" pdbx_component_id="3" pdbx_ens_id="1">
<VRPTx:beg_label_alt_id xsi:nil="true" />
<VRPTx:beg_label_asym_id>F</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>PRO</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>151</VRPTx:beg_label_seq_id>
<VRPTx:end_label_alt_id xsi:nil="true" />
<VRPTx:end_label_asym_id>F</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>GLY</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>179</VRPTx:end_label_seq_id>
</VRPTx:struct_ncs_dom_lim>
</VRPTx:struct_ncs_dom_limCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_ncs_dom_lim.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_ncs_ensType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_NCS_ENS category record information
about ensembles of domains related by noncrystallographic
symmetry. The point group of the ensemble when taken as a
whole may be specified, as well as any special aspects of the
ensemble that require description.
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
<VRPTx:struct_ncs_ensCategory>
<VRPTx:struct_ncs_ens id="en1">
<VRPTx:details> The ensemble represents the pseudo-twofold symmetry
between domains d1 and d2.</VRPTx:details>
</VRPTx:struct_ncs_ens>
</VRPTx:struct_ncs_ensCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_ncs_ens.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_ncs_ens_genType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_NCS_ENS_GEN category list domains
related by a noncrystallographic symmetry operation and
identify the operator.
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
<VRPTx:struct_ncs_ens_genCategory>
<VRPTx:struct_ncs_ens_gen dom_id_1="d1" dom_id_2="d2" ens_id="en1" oper_id="1"></VRPTx:struct_ncs_ens_gen>
</VRPTx:struct_ncs_ens_genCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_ncs_ens_gen.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_ncs_operType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_NCS_OPER category describe the
noncrystallographic symmetry operations.
Each operator is specified as a matrix and a subsequent
translation vector. Operators need not represent proper
rotations.
Example 1 - based on laboratory records for the protein NS1.
<VRPTx:struct_ncs_operCategory>
<VRPTx:struct_ncs_oper id="1">
<VRPTx:code>given</VRPTx:code>
<VRPTx:details> Matrix and translation vector for pseudo-twofold operation.</VRPTx:details>
<VRPTx:matrix11>0.247</VRPTx:matrix11>
<VRPTx:matrix12>0.935</VRPTx:matrix12>
<VRPTx:matrix13>0.256</VRPTx:matrix13>
<VRPTx:matrix21>0.929</VRPTx:matrix21>
<VRPTx:matrix22>0.153</VRPTx:matrix22>
<VRPTx:matrix23>0.337</VRPTx:matrix23>
<VRPTx:matrix31>0.276</VRPTx:matrix31>
<VRPTx:matrix32>0.321</VRPTx:matrix32>
<VRPTx:matrix33>-0.906</VRPTx:matrix33>
<VRPTx:vector1>-8.253</VRPTx:vector1>
<VRPTx:vector2>-11.743</VRPTx:vector2>
<VRPTx:vector3>-1.782</VRPTx:vector3>
</VRPTx:struct_ncs_oper>
</VRPTx:struct_ncs_operCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_ncs_oper.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_refType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_REF category allow the author of a
data block to relate the entities or biological units
described in the data block to information archived in external
databases.
For references to the sequence of a polymer, the value of
the data item attribute seq_align in category struct_ref is used to indicate
whether the correspondence between the sequence of the entity
or biological unit in the data block and the sequence in the
referenced database entry is 'complete' or 'partial'. If
this value is 'partial', the region (or regions) of the
alignment may be delimited using data items in the
STRUCT_REF_SEQ category.
Similarly, the value of attribute seq_dif in category struct_ref is used to indicate
whether the two sequences contain point differences. If the
value is 'yes', the differences may be identified and annotated
using data items in the STRUCT_REF_SEQ_DIF category.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:struct_refCategory>
<VRPTx:struct_ref id="1">
<VRPTx:biol_id xsi:nil="true" />
<VRPTx:db_code>12345</VRPTx:db_code>
<VRPTx:db_name>Genbank</VRPTx:db_name>
<VRPTx:details xsi:nil="true" />
<VRPTx:entity_id>1</VRPTx:entity_id>
<VRPTx:seq_align>entire</VRPTx:seq_align>
<VRPTx:seq_dif>yes</VRPTx:seq_dif>
</VRPTx:struct_ref>
<VRPTx:struct_ref id="2">
<VRPTx:biol_id>2</VRPTx:biol_id>
<VRPTx:db_code>1ABC</VRPTx:db_code>
<VRPTx:db_name>PDB</VRPTx:db_name>
<VRPTx:details> The structure of the closely related compound,
isobutyryl-pepstatin (pepstatin A) in complex with
rhizopuspepsin</VRPTx:details>
<VRPTx:entity_id xsi:nil="true" />
<VRPTx:seq_align xsi:nil="true" />
<VRPTx:seq_dif xsi:nil="true" />
</VRPTx:struct_ref>
</VRPTx:struct_refCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_ref.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_ref_seqType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_REF_SEQ category provide a mechanism
for indicating and annotating a region (or regions) of alignment
between the sequence of an entity or biological unit described
in the data block and the sequence in the referenced database
entry.
Example 1 - based on the sequence alignment of CHER from M. xantus
(36 to 288) and CHER from S. typhimurium (18 to 276).
<VRPTx:struct_ref_seqCategory>
<VRPTx:struct_ref_seq align_id="alg1">
<VRPTx:db_align_beg>18</VRPTx:db_align_beg>
<VRPTx:db_align_end>276</VRPTx:db_align_end>
<VRPTx:details> The alignment contains 3 gaps larger than 2 residues</VRPTx:details>
<VRPTx:ref_id>seqdb1</VRPTx:ref_id>
<VRPTx:seq_align_beg>36</VRPTx:seq_align_beg>
<VRPTx:seq_align_end>288</VRPTx:seq_align_end>
</VRPTx:struct_ref_seq>
</VRPTx:struct_ref_seqCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_ref_seq.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_ref_seq_difType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_REF_SEQ_DIF category provide a
mechanism for indicating and annotating point differences
between the sequence of the entity or biological unit described
in the data block and the sequence of the referenced database
entry.
Example 1 - based on laboratory records for CAP-DNA complex.
<VRPTx:struct_ref_seq_difCategory>
<VRPTx:struct_ref_seq_dif pdbx_ordinal="1">
<VRPTx:align_id>algn2</VRPTx:align_id>
<VRPTx:db_mon_id>GLU</VRPTx:db_mon_id>
<VRPTx:details> A point mutation was introduced in the CAP at position 181
substituting PHE for GLU.</VRPTx:details>
<VRPTx:mon_id>PHE</VRPTx:mon_id>
<VRPTx:seq_num>181</VRPTx:seq_num>
</VRPTx:struct_ref_seq_dif>
</VRPTx:struct_ref_seq_difCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_ref_seq_dif.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_sheetType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_SHEET category record details about
the beta-sheets.
Example 1 - simple beta-barrel.
N O N O N O N O N O N O
10--11--12--13--14--15--16--17--18--19--20 strand_a
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
30--31--32--33--34--35--36--37--38--39--40 strand_b
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
50--51--52--53--54--55--56--57--58--59--60 strand_c
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
70--71--72--73--74--75--76--77--78--79--80 strand_d
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
90--91--92--93--94--95--96--97--98--99-100 strand_e
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
110-111-112-113-114-115-116-117-118-119-120 strand_f
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
130-131-132-133-134-135-136-137-138-139-140 strand_g
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
150-151-152-153-154-155-156-157-158-159-160 strand_h
N O N O N O N O N O
/ \ / \ / \ / \ / \
<VRPTx:struct_sheetCategory>
<VRPTx:struct_sheet id="sheet_1">
<VRPTx:details xsi:nil="true" />
<VRPTx:number_strands>8</VRPTx:number_strands>
<VRPTx:type>beta-barrel</VRPTx:type>
</VRPTx:struct_sheet>
</VRPTx:struct_sheetCategory>
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
N O N O N O N O
-10--11--12--13--14--15--16--17--18-> strand_a
N O N O N O N O N O
| | | | | | | | | |
O N O N O N O N O N
<-119-118-117-116-115-114-113-112-111-110- strand_b
O N O N O N O N O N
\ / \ / \ / \ / \
O N O N O N O N O N O N
<-41--40--39--38--37--36--35--34--33--32--31--30- strand_c
O N O N O N O N O N O N
| | | | | | | | | | | |
N O N O N O N O N O N O
strand_d1 -50--51--52-> -90--91--92--93--95--95--96--97-> strand_d2
N O N O N O N O N O
| | | | | | | | | | | |
O N O N O N O N O N O N
<-80--79--78--77--76--75--74--73--72--71--70- strand_e
O N O N O N O N O N
<VRPTx:struct_sheetCategory>
<VRPTx:struct_sheet id="sheet_2">
<VRPTx:details>strand_d is in two pieces</VRPTx:details>
<VRPTx:number_strands>5</VRPTx:number_strands>
<VRPTx:type>five stranded, mixed-sense</VRPTx:type>
</VRPTx:struct_sheet>
</VRPTx:struct_sheetCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_sheet.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_sheet_hbondType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_SHEET_HBOND category record details
about the hydrogen bonding between residue ranges in a beta-
sheet. It is necessary to treat hydrogen bonding independently
of the designation of ranges, because the hydrogen bonding may
begin in different places for the interactions of a given strand
with the one preceding it and the one following it in the sheet.
Example 1 - simple beta-barrel.
<VRPTx:struct_sheet_hbondCategory>
<VRPTx:struct_sheet_hbond range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_1">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>11</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>19</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>30</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>40</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
<VRPTx:struct_sheet_hbond range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_1">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>31</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>39</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>50</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>60</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
<VRPTx:struct_sheet_hbond range_id_1="strand_c" range_id_2="strand_d" sheet_id="sheet_1">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>51</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>59</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>70</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>80</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
<VRPTx:struct_sheet_hbond range_id_1="strand_d" range_id_2="strand_e" sheet_id="sheet_1">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>71</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>89</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>90</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>100</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
<VRPTx:struct_sheet_hbond range_id_1="strand_e" range_id_2="strand_f" sheet_id="sheet_1">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>91</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>99</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>110</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>120</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
<VRPTx:struct_sheet_hbond range_id_1="strand_f" range_id_2="strand_g" sheet_id="sheet_1">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>111</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>119</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>130</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>140</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
<VRPTx:struct_sheet_hbond range_id_1="strand_g" range_id_2="strand_h" sheet_id="sheet_1">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>131</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>139</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>150</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>160</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
<VRPTx:struct_sheet_hbond range_id_1="strand_h" range_id_2="strand_a" sheet_id="sheet_1">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>151</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>159</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>10</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>180</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
</VRPTx:struct_sheet_hbondCategory>
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
<VRPTx:struct_sheet_hbondCategory>
<VRPTx:struct_sheet_hbond range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_2">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>20</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>18</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>119</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>111</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
<VRPTx:struct_sheet_hbond range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_2">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>110</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>N</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>118</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>33</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>O</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>41</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
<VRPTx:struct_sheet_hbond range_id_1="strand_c" range_id_2="strand_d1" sheet_id="sheet_2">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>38</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>40</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>52</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>50</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
<VRPTx:struct_sheet_hbond range_id_1="strand_c" range_id_2="strand_d2" sheet_id="sheet_2">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>30</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>36</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>96</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>90</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
<VRPTx:struct_sheet_hbond range_id_1="strand_d1" range_id_2="strand_e" sheet_id="sheet_2">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>51</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>51</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>80</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>80</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
<VRPTx:struct_sheet_hbond range_id_1="strand_d2" range_id_2="strand_e" sheet_id="sheet_2">
<VRPTx:range_1_beg_label_atom_id>N</VRPTx:range_1_beg_label_atom_id>
<VRPTx:range_1_beg_label_seq_id>91</VRPTx:range_1_beg_label_seq_id>
<VRPTx:range_1_end_label_atom_id>O</VRPTx:range_1_end_label_atom_id>
<VRPTx:range_1_end_label_seq_id>97</VRPTx:range_1_end_label_seq_id>
<VRPTx:range_2_beg_label_atom_id>O</VRPTx:range_2_beg_label_atom_id>
<VRPTx:range_2_beg_label_seq_id>76</VRPTx:range_2_beg_label_seq_id>
<VRPTx:range_2_end_label_atom_id>N</VRPTx:range_2_end_label_atom_id>
<VRPTx:range_2_end_label_seq_id>70</VRPTx:range_2_end_label_seq_id>
</VRPTx:struct_sheet_hbond>
</VRPTx:struct_sheet_hbondCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_sheet_hbond.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_sheet_orderType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_SHEET_ORDER category record details
about the order of the residue ranges that form a beta-sheet.
All order links are pairwise and the specified pairs are
assumed to be adjacent to one another in the sheet. These data
items are an alternative to the STRUCT_SHEET_TOPOLOGY data
items and they allow all manner of sheets to be described.
Example 1 - simple beta-barrel.
<VRPTx:struct_sheet_orderCategory>
<VRPTx:struct_sheet_order range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
<VRPTx:struct_sheet_order range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
<VRPTx:struct_sheet_order range_id_1="strand_c" range_id_2="strand_d" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
<VRPTx:struct_sheet_order range_id_1="strand_d" range_id_2="strand_e" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
<VRPTx:struct_sheet_order range_id_1="strand_e" range_id_2="strand_f" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
<VRPTx:struct_sheet_order range_id_1="strand_f" range_id_2="strand_g" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
<VRPTx:struct_sheet_order range_id_1="strand_g" range_id_2="strand_h" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
<VRPTx:struct_sheet_order range_id_1="strand_h" range_id_2="strand_a" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
</VRPTx:struct_sheet_orderCategory>
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
<VRPTx:struct_sheet_orderCategory>
<VRPTx:struct_sheet_order range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_2">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>anti-parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
<VRPTx:struct_sheet_order range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_2">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
<VRPTx:struct_sheet_order range_id_1="strand_c" range_id_2="strand_d1" sheet_id="sheet_2">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>anti-parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
<VRPTx:struct_sheet_order range_id_1="strand_c" range_id_2="strand_d2" sheet_id="sheet_2">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>anti-parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
<VRPTx:struct_sheet_order range_id_1="strand_d1" range_id_2="strand_e" sheet_id="sheet_2">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>anti-parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
<VRPTx:struct_sheet_order range_id_1="strand_d2" range_id_2="strand_e" sheet_id="sheet_2">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>anti-parallel</VRPTx:sense>
</VRPTx:struct_sheet_order>
</VRPTx:struct_sheet_orderCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_sheet_order.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_sheet_rangeType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_SHEET_RANGE category record details
about the residue ranges that form a beta-sheet. Residues are
included in a range if they made beta-sheet-type hydrogen-bonding
interactions with at least one adjacent strand and if there are
at least two residues in the range.
Example 1 - simple beta-barrel.
<VRPTx:struct_sheet_rangeCategory>
<VRPTx:struct_sheet_range id="strand_a" sheet_id="sheet_1">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>20</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>30</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
<VRPTx:struct_sheet_range id="strand_b" sheet_id="sheet_1">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>40</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>50</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
<VRPTx:struct_sheet_range id="strand_c" sheet_id="sheet_1">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>60</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>70</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
<VRPTx:struct_sheet_range id="strand_d" sheet_id="sheet_1">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>80</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>90</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
<VRPTx:struct_sheet_range id="strand_e" sheet_id="sheet_1">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>100</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>110</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
<VRPTx:struct_sheet_range id="strand_f" sheet_id="sheet_1">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>120</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>130</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
<VRPTx:struct_sheet_range id="strand_g" sheet_id="sheet_1">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>140</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>150</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
<VRPTx:struct_sheet_range id="strand_h" sheet_id="sheet_1">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>160</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>170</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
</VRPTx:struct_sheet_rangeCategory>
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
<VRPTx:struct_sheet_rangeCategory>
<VRPTx:struct_sheet_range id="strand_a" sheet_id="sheet_2">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>10</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>18</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
<VRPTx:struct_sheet_range id="strand_b" sheet_id="sheet_2">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>110</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>119</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
<VRPTx:struct_sheet_range id="strand_c" sheet_id="sheet_2">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>30</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>41</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
<VRPTx:struct_sheet_range id="strand_d1" sheet_id="sheet_2">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>50</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>52</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
<VRPTx:struct_sheet_range id="strand_d2" sheet_id="sheet_2">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>90</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>97</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
<VRPTx:struct_sheet_range id="strand_e" sheet_id="sheet_2">
<VRPTx:beg_label_asym_id>A</VRPTx:beg_label_asym_id>
<VRPTx:beg_label_comp_id>ala</VRPTx:beg_label_comp_id>
<VRPTx:beg_label_seq_id>70</VRPTx:beg_label_seq_id>
<VRPTx:end_label_asym_id>A</VRPTx:end_label_asym_id>
<VRPTx:end_label_comp_id>ala</VRPTx:end_label_comp_id>
<VRPTx:end_label_seq_id>80</VRPTx:end_label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_sheet_range>
</VRPTx:struct_sheet_rangeCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_sheet_range.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_sheet_topologyType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_SHEET_TOPOLOGY category record details
about the topology of the residue ranges that form a beta-sheet.
All topology links are pairwise and the specified pairs are
assumed to be successive in the amino-acid sequence. These
data items are useful in describing various simple and complex
folds, but they become inadequate when the strands in the sheet
come from more than one chain. The
STRUCT_SHEET_ORDER data items can be used to describe
single- and multiple-chain-containing sheets.
Example 1 - simple beta-barrel.
<VRPTx:struct_sheet_topologyCategory>
<VRPTx:struct_sheet_topology range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
<VRPTx:struct_sheet_topology range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
<VRPTx:struct_sheet_topology range_id_1="strand_c" range_id_2="strand_d" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
<VRPTx:struct_sheet_topology range_id_1="strand_d" range_id_2="strand_e" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
<VRPTx:struct_sheet_topology range_id_1="strand_e" range_id_2="strand_f" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
<VRPTx:struct_sheet_topology range_id_1="strand_f" range_id_2="strand_g" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
<VRPTx:struct_sheet_topology range_id_1="strand_g" range_id_2="strand_h" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
<VRPTx:struct_sheet_topology range_id_1="strand_h" range_id_2="strand_a" sheet_id="sheet_1">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
</VRPTx:struct_sheet_topologyCategory>
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
<VRPTx:struct_sheet_topologyCategory>
<VRPTx:struct_sheet_topology range_id_1="strand_a" range_id_2="strand_c" sheet_id="sheet_2">
<VRPTx:offset>+2</VRPTx:offset>
<VRPTx:sense>anti-parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
<VRPTx:struct_sheet_topology range_id_1="strand_c" range_id_2="strand_d1" sheet_id="sheet_2">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>anti-parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
<VRPTx:struct_sheet_topology range_id_1="strand_d1" range_id_2="strand_e" sheet_id="sheet_2">
<VRPTx:offset>+1</VRPTx:offset>
<VRPTx:sense>anti-parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
<VRPTx:struct_sheet_topology range_id_1="strand_e" range_id_2="strand_d2" sheet_id="sheet_2">
<VRPTx:offset>-1</VRPTx:offset>
<VRPTx:sense>anti-parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
<VRPTx:struct_sheet_topology range_id_1="strand_d2" range_id_2="strand_b" sheet_id="sheet_2">
<VRPTx:offset>-2</VRPTx:offset>
<VRPTx:sense>anti-parallel</VRPTx:sense>
</VRPTx:struct_sheet_topology>
</VRPTx:struct_sheet_topologyCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_sheet_topology.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_siteType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_SITE category record details about
portions of the structure that contribute to structurally
relevant sites (e.g. active sites, substrate-binding subsites,
metal-coordination sites).
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:struct_siteCategory>
<VRPTx:struct_site id="P2 site C">
<VRPTx:details> residues with a contact < 3.7 \%A to an atom in the P2
moiety of the inhibitor in the conformation with
_struct_asym.id = C</VRPTx:details>
</VRPTx:struct_site>
<VRPTx:struct_site id="P2 site D">
<VRPTx:details> residues with a contact < 3.7 \%A to an atom in the P1
moiety of the inhibitor in the conformation with
_struct_asym.id = D</VRPTx:details>
</VRPTx:struct_site>
</VRPTx:struct_siteCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_site.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_site_genType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_SITE_GEN category record details about
the generation of portions of the structure that contribute to
structurally relevant sites.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:struct_site_genCategory>
<VRPTx:struct_site_gen id="1" site_id="1">
<VRPTx:details xsi:nil="true" />
<VRPTx:label_asym_id>A</VRPTx:label_asym_id>
<VRPTx:label_comp_id>VAL</VRPTx:label_comp_id>
<VRPTx:label_seq_id>32</VRPTx:label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_site_gen>
<VRPTx:struct_site_gen id="2" site_id="1">
<VRPTx:details xsi:nil="true" />
<VRPTx:label_asym_id>A</VRPTx:label_asym_id>
<VRPTx:label_comp_id>ILE</VRPTx:label_comp_id>
<VRPTx:label_seq_id>47</VRPTx:label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_site_gen>
<VRPTx:struct_site_gen id="3" site_id="1">
<VRPTx:details xsi:nil="true" />
<VRPTx:label_asym_id>A</VRPTx:label_asym_id>
<VRPTx:label_comp_id>VAL</VRPTx:label_comp_id>
<VRPTx:label_seq_id>82</VRPTx:label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_site_gen>
<VRPTx:struct_site_gen id="4" site_id="1">
<VRPTx:details xsi:nil="true" />
<VRPTx:label_asym_id>A</VRPTx:label_asym_id>
<VRPTx:label_comp_id>ILE</VRPTx:label_comp_id>
<VRPTx:label_seq_id>84</VRPTx:label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_site_gen>
<VRPTx:struct_site_gen id="5" site_id="2">
<VRPTx:details xsi:nil="true" />
<VRPTx:label_asym_id>B</VRPTx:label_asym_id>
<VRPTx:label_comp_id>VAL</VRPTx:label_comp_id>
<VRPTx:label_seq_id>232</VRPTx:label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_site_gen>
<VRPTx:struct_site_gen id="6" site_id="2">
<VRPTx:details xsi:nil="true" />
<VRPTx:label_asym_id>B</VRPTx:label_asym_id>
<VRPTx:label_comp_id>ILE</VRPTx:label_comp_id>
<VRPTx:label_seq_id>247</VRPTx:label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_site_gen>
<VRPTx:struct_site_gen id="7" site_id="2">
<VRPTx:details xsi:nil="true" />
<VRPTx:label_asym_id>B</VRPTx:label_asym_id>
<VRPTx:label_comp_id>VAL</VRPTx:label_comp_id>
<VRPTx:label_seq_id>282</VRPTx:label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_site_gen>
<VRPTx:struct_site_gen id="8" site_id="2">
<VRPTx:details xsi:nil="true" />
<VRPTx:label_asym_id>B</VRPTx:label_asym_id>
<VRPTx:label_comp_id>ILE</VRPTx:label_comp_id>
<VRPTx:label_seq_id>284</VRPTx:label_seq_id>
<VRPTx:symmetry>1_555</VRPTx:symmetry>
</VRPTx:struct_site_gen>
</VRPTx:struct_site_genCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_site_gen.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | struct_site_viewType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the STRUCT_SITE_VIEW category record details
about how to draw and annotate an informative view of the
site.
Example 1 - based on NDB structure GDL001 by Coll, Aymami,
Van Der Marel, Van Boom, Rich & Wang
[Biochemistry (1989), 28, 310-320].
<VRPTx:struct_site_viewCategory>
<VRPTx:struct_site_view id="1">
<VRPTx:details> This view highlights the site of ATAT-Netropsin
interaction.</VRPTx:details>
<VRPTx:rot_matrix11>0.132</VRPTx:rot_matrix11>
<VRPTx:rot_matrix12>0.922</VRPTx:rot_matrix12>
<VRPTx:rot_matrix13>-0.363</VRPTx:rot_matrix13>
<VRPTx:rot_matrix21>0.131</VRPTx:rot_matrix21>
<VRPTx:rot_matrix22>-0.380</VRPTx:rot_matrix22>
<VRPTx:rot_matrix23>-0.916</VRPTx:rot_matrix23>
<VRPTx:rot_matrix31>-0.982</VRPTx:rot_matrix31>
<VRPTx:rot_matrix32>0.073</VRPTx:rot_matrix32>
<VRPTx:rot_matrix33>-0.172</VRPTx:rot_matrix33>
</VRPTx:struct_site_view>
</VRPTx:struct_site_viewCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_site_view.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | symmetryType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the SYMMETRY category record details about the
space-group symmetry.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:symmetryCategory>
<VRPTx:symmetry entry_id="5HVP">
<VRPTx:Int_Tables_number>18</VRPTx:Int_Tables_number>
<VRPTx:cell_setting>orthorhombic</VRPTx:cell_setting>
<VRPTx:space_group_name_H-M>P 21 21 2</VRPTx:space_group_name_H-M>
</VRPTx:symmetry>
</VRPTx:symmetryCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/symmetry.html. |
| Super-types: | None |
|---|---|
| Sub-types: | None |
| Name | symmetry_equivType |
|---|---|
| Abstract | no |
| Documentation |
Data items in the SYMMETRY_EQUIV category list the
symmetry-equivalent positions for the space group.
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
<VRPTx:symmetry_equivCategory>
<VRPTx:symmetry_equiv id="1">
<VRPTx:pos_as_xyz>+x,+y,+z</VRPTx:pos_as_xyz>
</VRPTx:symmetry_equiv>
<VRPTx:symmetry_equiv id="2">
<VRPTx:pos_as_xyz>-x,-y,z</VRPTx:pos_as_xyz>
</VRPTx:symmetry_equiv>
<VRPTx:symmetry_equiv id="3">
<VRPTx:pos_as_xyz>1/2+x,1/2-y,-z</VRPTx:pos_as_xyz>
</VRPTx:symmetry_equiv>
<VRPTx:symmetry_equiv id="4">
<VRPTx:pos_as_xyz>1/2-x,1/2+y,-z</VRPTx:pos_as_xyz>
</VRPTx:symmetry_equiv>
</VRPTx:symmetry_equivCategory>
More information at: http://pdbml.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/symmetry_equiv.html. |